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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Escherichia coli and UniProt Accession P0A6K3
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3.5.1.88 peptide deformylaseIUBMB Comments
Requires Fe(II). Also requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. Differs in substrate specifity from EC 3.5.1.31 (formylmethionine deformylase).
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Word Map
- 3.5.1.88
- actinonin
- medicine
-
n-formylated
-
deformylation
- eubacteria
-
hydroxamic
- drug development
-
formyltransferase
-
oxazolidinone
- catarrhalis
- linezolid
- moraxella
-
hexxh
- biotechnology
- synthesis
- agriculture
- molecular biology
- analysis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
peptide deformylase, hspdf, pdf-1, polypeptide deformylase, pdf1a, hppdf, pdf1b, pdf-2, vp16 pdf, tbpdf1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PDF
-
deformylase, peptide N-formylmethionine
-
-
-
-
hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
PDF
Polypeptide deformylase
-
-
-
-
PDF
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
deformylation
hydrolysis of amide bond
hydrolysis of amide bond
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
formyl-L-methionyl peptide amidohydrolase
Requires Fe(II). Also requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. Differs in substrate specifity from EC 3.5.1.31 (formylmethionine deformylase).
CAS REGISTRY NUMBER
COMMENTARY
369636-51-1
-
37289-08-0
-
9032-86-4
-
9054-98-2
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
formyl-L-methionyl peptide + H2O
formate + L-methionyl peptide
theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
?
formyl-Met-Ala-Ser + H2O
formate + Met-Ala-Ser
-
-
-
?
formyl-Met-Gly-Gly-CH3 + H2O
formate + Met-Gly-Gly-CH3
substrate used in QM-MM model
-
-
?
formylmethionine + H2O
formate + methionine
the smallest efficient substrate of PDF
-
-
?
N-formyl-L-Met-L-Leu-4-nitroanilide + H2O
formate + L-Met-L-Leu-4-nitroanilide
-
-
-
?
(RS)-phenylalanine nitrile + formate
(S)-N-formyl-phenylalanine nitrile
-
-
99% (S)-enantiomer
-
r
2-formyloxycaproylleucyl-p-nitroanilide + H2O
?
-
esterase activity, 10fold lower activity compared to N-formyl-Met-Leu-p-nitroanilide
-
-
?
formyl-L-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
-
?
formyl-Met-Ala-His-Ala-Ala-Gln + H2O
formate + Met-Ala-His-Ala-Ala-Gln
-
-
-
-
?
formyl-Met-Thr-Met-His-Thr-Thr + H2O
formate + Met-Thr-Met-His-Thr-Thr
-
-
-
-
?
N-(alpha-difluoroacetyl)-Met-Leu-p-nitroanilide + H2O
difluoroacetic acid + Met-Leu-p-nitroanilide
-
-
-
?
N-(alpha-fluoroacetyl)-Met-Leu-p-nitroanilide + H2O
fluoroacetic acid + Met-Leu-p-nitroanilide
-
-
-
?
N-formyl-1-(1-naphthyl)ethylamine + H2O
(1R)-1-naphthalen-1-ylethanamine + formate
-
-
90% (R)-enantiomer
-
?
N-formyl-3-amino-3-phenylpropionic acid + H2O
(R)-3-amino-3-phenylpropionic acid + formate
-
-
100% (R)-enantiomer
-
?
N-formyl-alpha-methyl-phenylglycine amide + H2O
(S)-alpha-methyl-phenylglycine amide + formate
-
-
100% (S)-enantiomer
-
?
N-formyl-beta-thiaphenylalanyl-Ala-Leu-4-nitroanilide + H2O
formate + beta-thiaphenylalanyl-Ala-Leu-4-nitroanilide
-
-
-
-
?
N-formyl-beta-thiaphenylalanyl-Lys-p-nitroanilide + H2O
formate + beta-thiaphenylalanyl-Lys-p-nitroanilide
N-formyl-beta-thiaphenylalanylleucyl 4-nitroanilide + H2O
formate + beta-thiaphenylalanylleucyl 4-nitroanilide
-
excellent substrate
-
?
N-formyl-His-Ala-Ser-Arg + H2O
formate + His-Ala-Ser-Arg
-
greatly attenuated activity, preference for N-terminal methionine
-
?
N-formyl-L-Met-D-Ala-Ser-Arg + H2O
formate + L-Met-D-Ala-Ser-Arg
-
strong requirement for L-methionine, but D-amino acids tolerated in other positions
-
?
N-formyl-L-Nle-L-Ala-L-Ser + H2O
formate + L-Nle-L-Ala-L-Ser
-
norleucine is the only excepted substitution for methionine
-
?
N-formyl-Leu-Tle-NHCH3 + H2O
(S)-Leu-(S)-Tle-NHCH3
-
Tle i.e. tert-leucine
Tle i.e. tert-leucine, 94% (S,S)-diastereomer
-
?
N-formyl-m-methoxyphenylalanine nitrile + H2O
(S)-m-methoxyphenylalanine nitrile + formate
-
-
99% (S)-enantiomer
-
?
N-formyl-Met-Ala-Phe-Tyr-beta-Ala-Arg + H2O
formate + Met-Ala-Phe-Tyr-beta-Ala-Arg
-
-
-
?
N-formyl-Met-Xaa-Xbb-Tyr + H2O
formate + Met-Xaa-Xbb-Tyr
-
consesus sequence for best substrates, Xaa: any amino acid except for Asp and Glu, Xbb: Lys, Arg, Tyr or Phe
-
?
N-formyl-Phe-Tyr-Phe + H2O
formate + Phe-Tyr-Phe
-
only N-terminal Phe can replace Met
-
?
N-formyl-Phe-Tyr-Phe-His-beta-Ala-Arg + H2O
formate + Phe-Tyr-Phe-His-beta-Ala-Arg
-
-
-
?
N-formyl-Phe-Tyr-Tyr + H2O
formate + Phe-Tyr-Tyr
-
only N-terminal Phe can replace Met
-
?
N-formyl-phenylalanine nitrile + H2O
(S)-phenylalanine nitrile + formate
-
-
98.8% (S)-enantiomer
-
?
N-formyl-phenylglycine + H2O
(S)-phenylglycine + formate
-
-
99.6% (S)-enantiomer
-
?
N-formyl-phenylglycine amide + H2O
(S)-phenylglycine amide + formate
-
-
99.7% (S)-enantiomer
-
?
N-formyl-phenylglycinol + H2O
(S)-phenylglycinol + formate
-
-
90.5-93.3% (S)-enantiomer, depending on method
-
?
N-formyl-tert-leucine amide + H2O
(S)-tert-leucine amide + formate
-
-
100% (S)-enantiomer
-
?
N-formyl-thiaphenylalanyl-peptide + H2O
formate + thiaphenylalanyl-peptide
-
-
-
-
?
N-formyl-valine nitrile + H2O
(S)-valine nitrile + formate
-
-
98.8% (S)-enantiomer
-
?
N-formylmethionylleucyl-amide + H2O
formate + methionylleucyl-amide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-Ala-Gly-Ser-Glu + H2O
formate + Ala-Gly-Ser-Glu
-
poor activity, preference of N-terminal methionine
-
?
N-formyl-Ala-Gly-Ser-Glu + H2O
formate + Ala-Gly-Ser-Glu
-
poor activity, preference of N-terminal methionine
-
?
N-formyl-beta-thiaphenylalanyl-Lys-p-nitroanilide + H2O
formate + beta-thiaphenylalanyl-Lys-p-nitroanilide
-
-
-
?
N-formyl-beta-thiaphenylalanyl-Lys-p-nitroanilide + H2O
formate + beta-thiaphenylalanyl-Lys-p-nitroanilide
-
-
-
?
N-formyl-beta-thiaphenylalanyl-peptide + H2O
formate + beta-thiaphenylalanyl-peptide
-
-
-
?
N-formyl-beta-thiaphenylalanyl-peptide + H2O
formate + beta-thiaphenylalanyl-peptide
-
significantly poorer substrate than N-formyl-thiaphenylalanylleucyl-p-nitroanilide
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
requires at least a dipeptide as substrate, increasing activity with increasing peptide length until it reaches the tetrapeptide
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
the enzyme is involved in maturation of proteins by cleaving the N-formyl group from N-blocked methionine polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
the enzyme is requiredfor the removal of the formyl group at the N-terminus of nascent polypeptide chains
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
posttranslational deformylation of N-formyl-Met-polypeptide
-
-
?
N-formyl-Met-Ala-Ser + H2O
formate + Met-Ala-Ser
-
higher activity than compared to di- or tetrapeptides
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
best substrate
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
best substrate
-
?
N-formyl-Met-Ser-Asn-Glu + H2O
formate + Met-Ser-Asn-Glu
-
decreasing activity for tetrapeptides
-
?
additional information
?
-
catalyzes the deformylation of nascent peptides in bacteria
-
-
?
additional information
?
-
-
catalyzes the deformylation of nascent peptides in bacteria
-
-
?
additional information
?
-
the removal of the formyl group from formylated methionine residues is facilitated by the action of peptide deformylase
-
-
?
additional information
?
-
-
the removal of the formyl group from formylated methionine residues is facilitated by the action of peptide deformylase
-
-
?
additional information
?
-
comparison of substrate specificity of the Escherichia coli PDF Vibrio phage Vp16 PDF
-
-
-
additional information
?
-
coupled enzyme activity assay with formate dehydrogenase
-
-
-
additional information
?
-
-
proposed reaction cycle of peptide deformylase
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
requires at least a dipeptide as substrate, increasing activity with increasing peptide length until it reaches the tetrapeptide
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
the enzyme is involved in maturation of proteins by cleaving the N-formyl group from N-blocked methionine polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
the enzyme is requiredfor the removal of the formyl group at the N-terminus of nascent polypeptide chains
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
posttranslational deformylation of N-formyl-Met-polypeptide
-
-
?
additional information
?
-
catalyzes the deformylation of nascent peptides in bacteria
-
-
?
additional information
?
-
-
catalyzes the deformylation of nascent peptides in bacteria
-
-
?
additional information
?
-
the removal of the formyl group from formylated methionine residues is facilitated by the action of peptide deformylase
-
-
?
additional information
?
-
-
the removal of the formyl group from formylated methionine residues is facilitated by the action of peptide deformylase
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Fe2+
Ni2+
Zn2+
Co2+
Fe
Fe2+
Ni2+
Zn2+
additional information
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
enzymatic activity of Escherichia coli PDF is retained after replacement of the active-site Fe2+ ion with Co2+
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
theoretically investigation of catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
required, catalytic metal ion, bound by Cys90, His132, and His136, metalloenzyme. Fe2+ leads to the lowest activation barriers for nucleophilic attack due to the ability of Fe2+ to act as a Lewis acid and thereby to more strongly coordinate to and activate the substrate carbonyl leading to a decrease in the energy barrier for the reaction. Fe2+ function analysis by using heteroscorpionate N2Sthiolate biomimetic ligand (L) complexed to Fe2+. The high-spin state for the Fe2+-L coordination complexes here has been shown to be the ground state. Reaction of Fe2+-L with formamide leading to formation of Fe2+-L-(formate) and ammonia
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
enzymatic activity of Escherichia coli PDF is retained after replacement of the active-site Fe2+ ion with Ni2+, the activity of the protein is not affected by Ni2+ concentrations up to 0.1 mM
Zn2+
His132 and His136 bind Zn2+ through their Nepsilon1 imidazole nitrogens
Zn2+
theoretically investigation of catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF
Fe
-
enzyme form 2 contains up to 1.0 iron atom per polypeptide - 0.77 Fe2+ and 0.2 Fe3+ per polypeptide. The iron is likely coordinated by His132, His136 and Cys90 in the protein
Ni2+
-
enzyme nearly retains its activity on substitution of the naturally occuring Fe2+ by Ni2+
Zn2+
-
enzyme form 1 contains approximately 1.0 Zn2+ per polypeptide chain, the zinc-containing protein 1 is likely formed during iron depletion caused by overexpression
additional information
theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
additional information
-
theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
additional information
preference for Fe2+ as the active site metal ion, versus, for example, Zn2+, Co2+, or N2+, despite Fe2+ being uncommon for this class of metalloenzymes and that PDF catalyzes a non-redox reaction. The difference in computed activation energies for deformylation between Fe2+, Co2+, and Zn2+ complexes with ligand L is fully consistent with experimental kinetics data for the Fe2+, Co2+, and Zn2+ forms of PDF as well as with the results from the earlier QM/MM computational studies
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(2R)-N-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-2-[[formyl(hydroxy)amino]methyl]hexanamide
-
(2R)-N-[(1S)-5-amino-1-(hexylcarbamoyl)pentyl]-2-[[formyl(hydroxy)amino]methyl]heptanamide
-
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide
an actinonin derivative
(2R)-N-[6-carbamimidamido-1-(naphthalen-2-yl)-2-oxohexan-3-yl]-2-(sulfanylmethyl)hexanamide
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[5-(trifluoromethyl)-4H-pyrazol-3-yl]-2,5-dihydro-1H-pyrrole-2-carboxamide
active against Staphylococcus aureus and Escherichia coli strains
(2S)-N1-(2-cyclopentylethyl)-N2-(4,5-dimethyl-1,3-thiazol-2-yl)-N1-[2-(hydroxyamino)-2-oxoethyl]pyrrolidine-1,2-dicarboxamide
-
(3R)-3-[3-[(1,3-benzothiazol-2-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
-
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
-
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[([1,1'-biphenyl]-4-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethoxy)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
-
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethyl)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
-
(3R)-N-hydroxy-3-[3-(4-nitrophenyl)-1,2,4-oxadiazol-5-yl]heptanamide
-
(3R)-N-hydroxy-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]heptanamide
-
(3R)-N-hydroxy-3-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]heptanamide
-
(5Z)-5-([2-[(E)-2-(dimethylamino)ethenesulfonyl]-6-phenylimidazo[2,1-b][1,3,4]thiadiazol-5-yl]methylidene)-1,3-thiazolidine-2,4-dione
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(1H-pyrazol-3-yl)-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methyl-3-[[4-(pyridin-3-yl)pyrimidin-2-yl]amino]phenyl)-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(5-methyl-1,3-thiazol-2-yl)-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-([1,2,4]triazolo[4,3-a]pyridin-3-yl)-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[3-(pyridin-3-yl)phenyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[3-[(pyrimidin-2-yl)amino]phenyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(pyridin-3-yl)pyrimidin-2-yl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[5-(pyridin-2-yl)-1,3,4-oxadiazol-2-yl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-N-(1H-benzimidazol-2-yl)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-N-(3-fluoropyridin-2-yl)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-N-(4-fluoropyridin-2-yl)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(6S)-N-(5-tert-butyl-1,2-oxazol-3-yl)-5-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-5-azaspiro[2.4]heptane-6-carboxamide
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,4-dimethoxybenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,5-dimethoxybenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,6-dichlorobenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2-chlorobenzylidene)thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(3,4,5-trimethoxybenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(3,4-dimethoxybenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-chlorobenzylidene)thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-fluorobenzylidene)thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-methoxybenzylidene) thiazolidine-2,4-dione
-
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-benzylidenethiazolidine-2,4-dione
-
1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide
-
1-[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]-N-hydroxymethanamine
-
2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide
-
2-amino-5-mercapto-1,3,4-thiadiazole
slow-binding inhibitor of PDF when dissolved only in dimethylformamide, but not in any other solvent, and aged (via the formation of a disulfide bond) to a dimeric form
2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxamide
-
2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide
-
2-[[formyl(hydroxy)amino]methyl]-N-[(5-methoxy-1H-benzimidazol-2-yl)methyl]hexanamide
potently active versus Escherichia coli strains and the Ni-PDF enzyme
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
-
4'-((3-fluoro-4-morpholinophenylamino)methyl)biphenyl-2-carbonitrile
-
4'-((6-methoxybenzothiazol-2-ylamino)methyl)biphenyl-2-carbonitrile
-
4'-(2-ethyl-6,8-dimethylimidazo[1,2-b]pyridazin-3-yl)[1,1'-biphenyl]-2-carboxylic acid
-
4'-([(5Z)-2,4-dioxo-5-[(3,4,5-trimethoxyphenyl)methylidene]-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(2,4-dimethoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(2,5-dimethoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(2,6-dichlorophenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(2-chlorophenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(3,4-dimethoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(4-chlorophenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(4-fluorophenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-([(5Z)-5-[(4-methoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl]methyl)[1,1'-biphenyl]-2-carbonitrile
-
4'-[(2-ethyl-6,8-dimethyl-3,5-dihydroimidazo[1,2-b]pyridazin-3-yl)methyl][1,1'-biphenyl]-2-carboxylic acid
-
4'-[[(5Z)-5-benzylidene-2,4-dioxo-1,3-thiazolidin-3-yl]methyl][1,1'-biphenyl]-2-carbonitrile
-
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl hydrogen carbonate
-
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
-
4-[(Z)-[3-(2-chlorobenzoyl)-2,4-dioxo-1,3-thiazolidin-5-ylidene]methyl]-N-(4-phenyl-1,3-thiazol-2-yl)benzene-1-sulfonamide
-
5,5'-disulfanediyldi(1,3,4-thiadiazol-2-amine)
dimerization of two 2-amino-5-mercapto-1,3,4-thiadiazole molecules via the dithiol linkage forming bis-AMT
5-([[(1-benzothiophen-2-yl)methyl]sulfanyl]methyl)-N-hydroxy-1,2-oxazole-3-carboxamide
poor antibacterial activity
5-amino-1,3,4-thiadiazole-2-thiol
a slow-binding inhibitor of Escherichia coli Ni-PDF inhibitor upon aging
5-bromo-7-methyl-2-propyl-3-[[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-3H-imidazo[4,5-b]pyridine
-
5-chloro-2-propyl-3-[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]-3H-imidazo[4,5-b]pyridine
-
benzyl 5-bromo-3-[2-(hydroxyamino)-2-oxoethyl]-1H-indole-1-carboxylate
-
ethyl 2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxylate
-
isoxazole-3-hydroxamic acids
23 different compounds were synthesized and compared to the inhibitory activity of actinonin
-
macrolactin N
isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains
methyl N-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinate
-
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cycloheptadec-6-yl)-methyl-N-hydroxy-formamide
-
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclohexadec-6-yl)-methyl-N-hydroxy-formamide
-
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cycloicos-6-yl)-methyl-N-hydroxy-formamide
-
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclopentadec-6-yl)-methyl-N-hydroxy-formamide
-
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclotridec-6-yl)-methyl-N-hydroxy-formamide
-
N-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,3lambda4,2,4-benzodithiadiazin-2-yl)acetamide
-
N-[(2R)-2-(cyclopentylmethyl)-3-[2-(furan-2-carbonyl)-1,2-diazinan-1-yl]-3-oxopropyl]-N-hydroxyformamide
-
N-[3-(4-acetamidobutyl)-2,5-dioxo-1,4-diaza-cyclopentadec-6-yl]methyl-N-hydroxy-formamide
-
N-[3-(4-aminobutyl)-2,5-dioxo-1,4-diazacycloicos-6-yl]methyl-N-hydroxyformamide
-
N-[3-(4-aminobutyl)-2,5-dioxo-1,4-diazacyclopentadec-6-yl]methyl-N-hydroxyformamide
-
N-[4'-(2-cyclopropyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)[1,1'-biphenyl]-2-sulfonyl]benzamide
-
N-[[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]methyl]-N-hydroxyacetamide
-
N-[[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]methyl]-N-hydroxyformamide
-
N2-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-phenyl-L-lysinamide
-
N2-[(2R)-2-[[hydroxy(oxo)-lambda5-phosphanyl]oxy]hexanoyl]-N-(4-nitrophenyl)-D-leucinamide
-
N2-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinamide
-
Ni2+
addition of 1 mM Ni2+ increases the PDF activity by 70%, with 20 mM Ni2+, the activity decreases by 23% compared with the low Ni2+ concentration
(2R)-N-[(2S)-1-{4-[(2H-1,3-benzodioxol-5-yl)methyl]piperazin-1-yl}-3,3-dimethyl-1-oxobutan-2-yl]-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-nitrophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(5-methyl-1,3-thiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(pyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[(1R)-1-phenylethyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[(1S)-1-phenylethyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-1-{(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl}-N-(5-methyl-1,3-thiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(2-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(2-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(3-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(4-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(4-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(4-fluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(5-fluoro-1-oxidopyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-(5-fluoropyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S)-N-cyclopropyl-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(2S,3aR,7aS)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylpyridin-2-yl)octahydro-1H-indole-2-carboxamide
-
-
(2S,3aR,7aS)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)octahydro-1H-indole-2-carboxamide
-
-
(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-fluoropyridin-2-yl)octahydro-1H-indole-2-carboxamide
-
-
(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-methylpyridin-2-yl)octahydro-1H-indole-2-carboxamide
-
-
(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-methylthiazol-2-yl)octahydro-1H-indole-2-carboxamide
-
-
(2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-fluoro-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
-
-
(2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-methyl-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
-
-
(2S,4S)-4-fluoro-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
-
-
(E)-1,5-dimethyl-2-phenyl-4-((5-styryl-1,3,4-thiadiazol-2-yl)amino-1,2-dihydro-3H-pyrazole-3-one)
-
-
(RS)- and (SR)-3-[(RS)-benzenesulfinyl]heptanoic acid hydroxyamide
-
mixture of both components, IC50: 0.0001 mM, possible antimicrobial agent
(RS)-3-(phenylsulfonyl)heptanoic acid hydroxyamide
-
IC50: 0.035 micro molar, possible antimicrobial agent
(S)-1-((R)-2-(((formyl-hydroxyamino)methyl)hexanoyl)-N-(5-fluoro-1-oxido-pyridin)-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(2-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(2-chlorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(3-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(4-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(4-chlorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((formyl-hydroxyamino)methyl)hexanoyl)-N-(5-fluoropyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylene-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylene-N-phenylpyrrolidine-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-((R)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-((S)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(4-nitrophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(pyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-Nphenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-((S)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(4-fluorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-fluoropyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-2-O-(H-phosphonoxy)-L-caproyl-L-Leu-p-nitroanilide
-
similar inhibition of Fe2+- and Co2+-bound enzyme
(S)-N-(4-fluorophenyl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(S)-N-(4-fluorophenyl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamide
-
-
(S)-N-(5-fluoropyridin-2-yl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamide
-
-
(S)-N-cyclopropyl-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
-
-
(Z)-4-hydroxy-3-(5-((4-(phenyldiazenyl) phenyl) amino)-1,3,4-thiadiazol-2-yl)benzene sulfonic acid
-
-
(Z)-5-(3,4-dimethoxyphenyl)-N-(4-(phenyl diazenyl) phenyl)-1,3,4-thiadiazol-2-amine
-
-
2-((2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-fluoropyrrolidine-2-carboxamido)-5-fluoropyridine 1-oxide
-
-
2-((2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-methylpyrrolidine-2-carboxamido)-5-fluoropyridine 1-oxide
-
-
2-((S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamido)-5-fluoropyridine 1-oxide
-
-
2-(1-benzyl-5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.002 mM
2-(1-butyl-5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.00059 mM
2-(2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.00076 mM
2-(5-bromo-1-cyclopropyl-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.000069 mM
2-(5-bromo-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.000098 mM
2-(5-bromo-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
-
IC50: 0.000049 mM
2-(5-chloro-1-cyclopropyl-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.00011 mM
2-(5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
inhibitor shows good selectivity for peptide deformylase over several endoproteases including matrix metalloproteases, however it shows only weak antibacterial activity. IC50: 0.00012 mM
2-(5-chloro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
-
inhibitor shows good selectivity for peptide deformylase over several endoproteases including matrix metalloproteases, however it shows only weak antibacterial activity. IC50: 0.00031 mM
2-(5-chloro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetohydrazide
-
IC50: 0.027 mM
2-(5-fluoro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
-
IC50: 0.00087 mM
2-(5-fluoro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
-
IC50: 0.00087 mM
2-butyl-5,7-dimethyl-3-[2''-(1H-tetrazol-5-ylmethyl)-[1,1',4',1'']terphenyl-4-yl]-3H-imidazo[4,5-b]pyridine
-
belongs to a class of angiotensin II receptor antagonists, potent inhibitor, IC50: 0.0076 mM
2-[(12R,17aS)-1,13-dioxohexadecahydro-1H-pyrrolo[1,2-a][1,4]diazacyclopentadecin-12-yl]-N-hydroxyacetamide
-
-
2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide
-
-
2-[2,2-dioxido-5-(trifluoromethyl)-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl]-N-hydroxyacetamide
-
IC50: 0.00013 mM
2-[5-chloro-2,2-dioxido-1-(3-phenylpropyl)-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl]-N-hydroxyacetamide
-
IC50: 0.00029 mM
3-(5-((4H-1,2,4-triazol-4-yl)amino)-1,3,4-thiadiazol-2-yl)-4-hydroxy benzenesulfonic acid
-
-
3-(5-((furan-2-ylmethyl)amino)-1,3,4-thiadiazole-2-yl)-4-hydroxybenzenesulfonic acid
-
-
3-(5-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]-4H-1,2,4-triazol-3-yl)-4-hydroxybenzenesulfonic acid
-
-
3-[5'-benzyl-2'-(1H-tetrazol-5-yl)-biphenyl-4-yl]-2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridine
-
potent inhibitor, IC50: 0.0342 mM, the acidic moiety forms direct ionic interactions with active site metal cation
4-((5-(3,4-dimethoxyphenyl)-1,3,4-thiadiazol-2-yl)amino)-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
-
-
4-hydroxy-3-(5-((5-methylisoxazol-3-yl)amino)-1,3,4-thiadiazol-2-yl)benzenesulfonic acid
-
-
4-hydroxy-3-(5-[(4-methylpyridin-2-yl)amino]-4H-1,2,4-triazol-3-yl)benzenesulfonic acid
-
-
5-(3,4-dimethoxyphenyl)-N-(4-methylpyridine-2-yl)-1,3,4-thiadiazol-2-amine
-
-
5-(3,4-dimethoxyphenyl)-N-(4H-1,2,4-triazol-4-yl)-1,3,4-thiadiazol-2-amine
-
-
5-bromo-3-hydroxycarbamoylmethylindole-1-carboxylic acid benzyl ester
-
MIC is 0.12 mg/ml
5-chloro-2-propyl-3-[2''-(1H-tetrazol-5-ylmethyl)-[1,1',4',1'']terphenyl-4-yl]-3H-imidazo[4,5-b]pyridine
-
belongs to a broad class of angiotensin II receptor antagonists, potent competitive inhibitor, IC50: 0.0039 mM, the acidic moiety forms direct ionic interactions with active site metal cation
5-fluoro-2-((2S,4S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylpyrrolidine-2-carboxamido)pyridine 1-oxide
-
-
5-fluoro-2-((2S,4S)-4-fluoro-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)pyrrolidine-2-carboxamido)pyridine1-oxide
-
-
5-fluoro-2-((S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamido)pyridine 1-oxide
-
-
butyl {[4'-(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)-5-(2-methylbutan-2-yl)biphenyl-2-yl]sulfonyl}carbamate
-
competitive inhibition, IC50: 0.015 mM, the acidic moiety forms direct ionic interactions with active site metal cation
imino[(5-methoxy-5-oxo-4-[2-(sulfanylmethyl)hexanoyl]aminopentyl)amino]methaneamine
-
-
N-((R)-2-(cyclopentylmethyl)-3-((S)-2-(morpholine-4-carbonyl)-2,5-dihydro-1H-pyrrol-1-yl)-3-oxopropyl)-N-hydroxyformamide
-
-
N-(1-benzenesulfonyl-5-bromo-2-methyl-1H-indol-3-ylmethyl)-N-hydroxyformamide
-
MIC is 0.065 mg/ml
N-(4-((Z)-phenyldiazenyl) phenyl)-5-((Z)-styryl)-1,3,4-thiadiazol-2-amine
-
-
N-(5-(3,4-dimethoxy phenyl)-1,3,4-thiadiazol-2-yl)-5-methylisoxazol-3-amine
-
-
N-(5-fluoro-1-hydroxypyridin-1-ium-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]prolinamide
-
-
N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
i.e. SB 543668, IC50: 0.00115 mM
N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
-
IC50: 0.0029 mM
N-hydroxy-2-[2-oxo-5-(trifluoromethyl)-1,4-dihydroquinazolin-3(2H)-yl]acetamide
-
IC50: 0.00023 mM
N-hydroxy-N-((R)-2-((S)-2-(morpholine-4-carbonyl)-2,5-dihydro-1H-pyrrole-1-carbonyl)hexyl)formamide
-
-
N-hydroxy-N-((R)-2-((S)-4-methylene-2-(morpholine-4-carbonyl)pyrrolidine-1-carbonyl)hexyl)formamide
-
-
N-hydroxy-N-[(2R)-2-[[(2S)-2-(morpholin-4-ylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]carbonyl]hexyl]formamide
-
-
N-hydroxy-N-[3-(6-methylpyridine-2-yl)propyl]formamide
-
i.e. SB 505684, IC50: 0.0028 mM
N-[(2R)-2-(cyclopentylmethyl)-3-(2-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}hydrazinyl)-3-oxopropyl]-N-hydroxyformamide
-
-
N-[4-(trifluoromethyl)benzoyl]-L-Met
-
time-dependent inhibition of zinc and cobalt deformylase, inhibition of full-length Co-PDF is competitive
N-[4-(trifluoromethyl)benzoyl]-L-Met hydrazide
-
time-dependent inhibition of zinc and cobalt deformylase
polylethylene glycol
-
competitive inhibitor with respect to formylmethionine
-
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
broadly active versus Escherichia coli and Bacillus subtilis strains
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
broadly active versus Escherichia coli and Bacillus subtilis strains
6-chloro-2-propyl-1-[[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-1H-benzimidazole
-
6-chloro-2-propyl-1-[[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-1H-benzimidazole
-
-
actinonin
i.e. 3-[(1-[[2-(hydroxymethyl)-1-pyrrolidinyl]carbonyl]-2-methylpropyl)carbamoyl]octanohydroxamic acid, a naturally occurring potent PDF inhibitor
actinonin
competitive inhibitor, binding in a two-step mechanism, determination and comparison of the three-dimensional structure of Escherichia coli PDF bound to actinonin
additional information
theoretical study of Escherichia coli peptide deformylase inhibition by several drugs
-
additional information
-
theoretical study of Escherichia coli peptide deformylase inhibition by several drugs
-
additional information
biphenyl tetrazole-thiazolidinediones as bacterial peptide deformylase inhibitors: synthesis, biological evaluations, and molecular docking study, overview. MIC values with Escherichia coli and Bacillus subtilis cells
-
additional information
-
biphenyl tetrazole-thiazolidinediones as bacterial peptide deformylase inhibitors: synthesis, biological evaluations, and molecular docking study, overview. MIC values with Escherichia coli and Bacillus subtilis cells
-
additional information
cacterial peptide deformylase inhibition of cyano-substituted biaryl analogues, synthesis, in vitro biological evaluation, molecular docking study, and in silico ADME (absorption, distribution, metabolism, excretion) prediction, overview. Structure-activity studies. In vitro antibacterial activity analysis of the synthesized compounds against Escherichia coli strain NCIM-2256 and Bacillus subtilis strain NCIM-2063
-
additional information
-
cacterial peptide deformylase inhibition of cyano-substituted biaryl analogues, synthesis, in vitro biological evaluation, molecular docking study, and in silico ADME (absorption, distribution, metabolism, excretion) prediction, overview. Structure-activity studies. In vitro antibacterial activity analysis of the synthesized compounds against Escherichia coli strain NCIM-2256 and Bacillus subtilis strain NCIM-2063
-
additional information
design and synthesis of 4-((5-benzylidene-2,4-dioxothiazolidin-3-yl)methyl)biphenyl-2-carbonitrile analogues as bacterial peptide deformylase inhibitors, structure-activity relationship analysis, docking study, detailed overview. Antibacterial activity compared to standard ampicillin, MIC values for Escherichia coli and Bacillus subtilis
-
additional information
-
design and synthesis of 4-((5-benzylidene-2,4-dioxothiazolidin-3-yl)methyl)biphenyl-2-carbonitrile analogues as bacterial peptide deformylase inhibitors, structure-activity relationship analysis, docking study, detailed overview. Antibacterial activity compared to standard ampicillin, MIC values for Escherichia coli and Bacillus subtilis
-
additional information
different classes of PDF inhibitors, structures, and molecular modeling studies, overview. Poor inhibition by 23 and 24
-
additional information
inhibitor design with the enzyme as model, structure-activity relationship analysis, overview. Design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug-resistant clinical isolate. Determination of minimal inhibitory concentrations of oxadiazole compounds for antibacterial activity on Escherichia coli strains. Three-dimensional comparison of the binding between various PDF inhibitors and actinonin
-
additional information
ligand and structure-based approaches for identification of peptide deformylase inhibitors as antibacterial drugs, development of pharmacophore models, molecular docking using the crystal structure of Escherichia coli PDF (PDB ID 1G2A), in silico pharmacokinetic and toxicity prediction studies, overview. Computer-aided drug design (CADD)
-
additional information
-
ligand and structure-based approaches for identification of peptide deformylase inhibitors as antibacterial drugs, development of pharmacophore models, molecular docking using the crystal structure of Escherichia coli PDF (PDB ID 1G2A), in silico pharmacokinetic and toxicity prediction studies, overview. Computer-aided drug design (CADD)
-
additional information
molecular docking and screening of designed small molecule ligands, a critical arginine residue in peptide deformylase for spiro cyclopropyl PDF inhibitor's extra hydrophobic binding is identified. Compund synthesis and structure confirmation by LC-MS, 1H NMR, 13C NMR, and HRMS. The compounds are evaluated through in vitro antibacterial activity assay, some are further subjected to in vivo rat pharmacokinetic assessment. Spiro cyclopropyl proline N-formyl hydroxylamines, and especially the bioisosteric azoles, are a promising class of PDF inhibitors
-
additional information
-
the results of the study may provide the basis for the design of more potent and selective deformylase inhibitors as potential antibacterial agents
-
additional information
-
synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria, MIC values, structure-activity relationships, overview
-
additional information
-
molecular docking studies of 1,3,4-thiadiazoles as peptide deformylase inhibitors, molecular modeling of the enzyme binding mode, docking study using the structure of Escherichia coli enzyme (PDB ID 1G27) complexed with inhibitor Bb-3497, overview. The compounds are potential antibacterial agents. Enzyme binding involves residues Gly45, Gly89, Glu95, Cys90, Leu91, Leu46, Met 38, Ile44, and Ile128
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KCl
-
2fold increase within 0-0.5 M, beyond 0.5 M smaller extend of increase
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.052
N-formyl-L-Met-L-Leu-4-nitroanilide
in 50 mM potassium phosphate buffer, pH 7.0, temperature not specified in the publication
0.018
N-formyl-beta-thiaphenylalanyl-lysyl-p-nitroanilide
-
recombinant mutant E133D Co2+-bound enzyme
0.2
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Ni2+
70
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Zn2+
0.027
N-formyl-beta-thiaphenylalanyl-Lys-p-nitroanilide
-
recombinant Fe2+-bound enzyme
0.03
N-formyl-beta-thiaphenylalanyl-Lys-p-nitroanilide
-
recombinant Co2+-bound enzyme
0.028
N-formylmethionyl-Leu-p-nitroanilide
-
recombinant mutant E133D Co2+-bound enzyme
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
reaction kinetics and thermodynamics, modeling, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5.6
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Zn2+
34
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Ni2+
4.2
N-formylmethionylleucyl-p-nitroanilide
-
recombinant mutant E133D Co2+-bound enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.08
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Zn2+
170
formyl-Met-Ala-Ser
pH 4.5, 37°C, recombinant enzyme with bound Ni2+
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000011
(2R)-N-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-2-[[formyl(hydroxy)amino]methyl]hexanamide
DPPI assay
0.000074
(2R)-N-[(1S)-5-amino-1-(hexylcarbamoyl)pentyl]-2-[[formyl(hydroxy)amino]methyl]heptanamide
DPPI assay
0.000076
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
pH 7.5, 37°C, recombinant enzyme
0.000035
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
pH 7.5, 37°C, recombinant enzyme
0.00008
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
pH 7.5, 37°C, recombinant enzyme
0.000025
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
pH 7.5, 37°C, recombinant enzyme
0.000031
(3R)-3-[3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
pH 7.5, 37°C, recombinant enzyme
0.000073
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethoxy)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
pH 7.5, 37°C, recombinant enzyme
0.00008
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethyl)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
pH 7.5, 37°C, recombinant enzyme
0.000029
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
pH 7.5, 37°C, recombinant enzyme
0.000769
2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
pH 7.5, 37°C, recombinant enzyme
0.000047
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
pH 7.5, 37°C, recombinant enzyme
0.17
2-amino-5-mercapto-1,3,4-thiadiazole
in 50 mM potassium phosphate buffer, pH 7.0, temperature not specified in the publication
0.000833
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
pH 7.5, 37°C, recombinant enzyme
0.000049
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
pH 7.5, 37°C, recombinant enzyme
0.000077
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cycloheptadec-6-yl)-methyl-N-hydroxy-formamide
DPPI assay
0.000096
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclohexadec-6-yl)-methyl-N-hydroxy-formamide
DPPI assay
0.0021
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cycloicos-6-yl)-methyl-N-hydroxy-formamide
DPPI assay
0.000109
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclopentadec-6-yl)-methyl-N-hydroxy-formamide
DPPI assay
0.000063
N-(3-tert-butyl-2,5-dioxo-1,4-diaza-cyclotridec-6-yl)-methyl-N-hydroxy-formamide
DPPI assay
0.00071
N-[3-(4-acetamidobutyl)-2,5-dioxo-1,4-diaza-cyclopentadec-6-yl]methyl-N-hydroxy-formamide
DPPI assay
0.000258
N-[3-(4-aminobutyl)-2,5-dioxo-1,4-diazacycloicos-6-yl]methyl-N-hydroxyformamide
DPPI assay
0.000092
N-[3-(4-aminobutyl)-2,5-dioxo-1,4-diazacyclopentadec-6-yl]methyl-N-hydroxyformamide
DPPI assay
0.000023
N2-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-phenyl-L-lysinamide
DPPI assay
0.0012
3-[5'-benzyl-2'-(1H-tetrazol-5-yl)-biphenyl-4-yl]-2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridine
-
-
0.006
butyl {[4'-(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)-5-(2-methylbutan-2-yl)biphenyl-2-yl]sulfonyl}carbamate
-
-
0.2
N-[4-(trifluoromethyl)benzoyl]-L-methionyl hydrazide
-
full-lenfth Co-PDF
0.052
methyl-1-(sulfanylmethyl)hexanoate
-
wild-type enzyme and mutant enzyme E88A
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000007
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.00104
(2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.00003
(3R)-3-[3-[(1,3-benzothiazol-2-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000006
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000017
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000007
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00001
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000004
(3R)-3-[3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000025
(3R)-3-[3-[([1,1'-biphenyl]-4-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000155
(3R)-N-hydroxy-3-(3-phenyl-1,2,4-oxadiazol-5-yl)heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000078
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethoxy)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000014
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethyl)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00019
(3R)-N-hydroxy-3-(4-phenyl-1,3-oxazol-2-yl)heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00016
(3R)-N-hydroxy-3-[3-(4-nitrophenyl)-1,2,4-oxadiazol-5-yl]heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000027
(3R)-N-hydroxy-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000215
(3R)-N-hydroxy-3-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]heptanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.0355
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,4-dimethoxybenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.0265
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,5-dimethoxybenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01725
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2,6-dichlorobenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.018
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(2-chlorobenzylidene)thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.033
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(3,4,5-trimethoxybenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.02675
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(3,4-dimethoxybenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01625
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-chlorobenzylidene)thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.02625
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-fluorobenzylidene)thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.026
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-(4-methoxybenzylidene) thiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.0205
(E)-3-((20-(1H-tetrazol-5-yl)biphenyl-4-yl)methyl)-5-benzylidenethiazolidine-2,4-dione
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.00002
1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.00012
2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide
Escherichia coli
pH and temperature not specified in the publication
0.00048
2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00074
2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00011
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.033
4'-((2-hydroxyphenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01566
4'-((2-nitrophenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.02091
4'-((3-(trifluoromethyl)phenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.0425
4'-((3-fluoro-4-morpholinophenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.025
4'-((3-nitrophenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.0335
4'-((4-(trifluoromethyl)phenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.05116
4'-((4-carboxyphenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.02825
4'-((4-chloro-2-nitrophenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.03458
4'-((4-hydroxyphenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.05075
4'-((4H-1,2,4-triazol-4-ylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.02775
4'-((6-methoxybenzothiazol-2-ylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01316
4'-((phenylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01916
4'-((pyrazin-2-ylamino)methyl)biphenyl-2-carbonitrile
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.0039
4'-(2-ethyl-6,8-dimethylimidazo[1,2-b]pyridazin-3-yl)[1,1'-biphenyl]-2-carboxylic acid
Escherichia coli
pH and temperature not specified in the publication
0.000075
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl hydrogen carbonate
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00002
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.0037
5,5'-disulfanediyldi(1,3,4-thiadiazol-2-amine)
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.0034
5-([[(1-benzothiophen-2-yl)methyl]sulfanyl]methyl)-N-hydroxy-1,2-oxazole-3-carboxamide
Escherichia coli
pH and temperature not specified in the publication
0.129
5-amino-1,3,4-thiadiazole-2-thiol
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.0162
5-bromo-7-methyl-2-propyl-3-[[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-3H-imidazo[4,5-b]pyridine
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.01
5-chloro-2-propyl-3-[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]-3H-imidazo[4,5-b]pyridine
Escherichia coli
pH and temperature not specified in the publication
0.0039
6-chloro-2-propyl-1-[[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl]-1H-benzimidazole
Escherichia coli
pH 7.4, 30°C, recombinant enzyme
0.026
calpeptin
Escherichia coli
pH and temperature not specified in the publication, versus Fe-PDF enzyme
0.00011
ethyl 2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxylate
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00033
methyl N-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinate
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.00031
N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
Escherichia coli
pH and temperature not specified in the publication
0.000005
N-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,3lambda4,2,4-benzodithiadiazin-2-yl)acetamide
Escherichia coli
pH and temperature not specified in the publication
0.000005
N-[(2R)-2-(cyclopentylmethyl)-3-[2-(furan-2-carbonyl)-1,2-diazinan-1-yl]-3-oxopropyl]-N-hydroxyformamide
Escherichia coli
pH and temperature not specified in the publication, versus Ni-PDF enzyme
0.0228
N-[4'-(2-cyclopropyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)[1,1'-biphenyl]-2-sulfonyl]benzamide
Escherichia coli
pH and temperature not specified in the publication
0.076
N2-[(2R)-2-[[hydroxy(oxo)-lambda5-phosphanyl]oxy]hexanoyl]-N-(4-nitrophenyl)-D-leucinamide
Escherichia coli
pH and temperature not specified in the publication, versus Fe-PDF enzyme
0.00042
N2-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.0259
(E)-1,5-dimethyl-2-phenyl-4-((5-styryl-1,3,4-thiadiazol-2-yl)amino-1,2-dihydro-3H-pyrazole-3-one)
Escherichia coli
-
pH and temperature not specified in the publication
0.0284
(E)-5-methyl-N-(5-styryl-1,3,4-thiadiazole-2-yl)isoxazol-3-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0224
(E)-5-styryl-N-(4H-1,2,4-triazol-4-yl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0652
(E)-N-(furan-2-ylmethyl)-5-styryl-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0001
(RS)- and (SR)-3-[(RS)-benzenesulfinyl]heptanoic acid hydroxyamide
Escherichia coli
-
mixture of both components, IC50: 0.0001 mM, possible antimicrobial agent
0.000035
(RS)-3-(phenylsulfonyl)heptanoic acid hydroxyamide
Escherichia coli
-
IC50: 0.035 micro molar, possible antimicrobial agent
0.323
(Z)-4-hydroxy-3-(5-((4-(phenyldiazenyl) phenyl) amino)-1,3,4-thiadiazol-2-yl)benzene sulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.2061
(Z)-5-(3,4-dimethoxyphenyl)-N-(4-(phenyl diazenyl) phenyl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0277
(Z)-N-(4-methylpyridine-2-yl)-5-styryl-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.002
2-(1-benzyl-5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.002 mM
0.00059
2-(1-butyl-5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00059 mM
0.00076
2-(2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00076 mM
0.000069
2-(5-bromo-1-cyclopropyl-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.000069 mM
0.000098
2-(5-bromo-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.000098 mM
0.000049
2-(5-bromo-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.000049 mM
0.00011
2-(5-chloro-1-cyclopropyl-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00011 mM
0.00012
2-(5-chloro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
inhibitor shows good selectivity for peptide deformylase over several endoproteases including matrix metalloproteases, however it shows only weak antibacterial activity. IC50: 0.00012 mM
0.00031
2-(5-chloro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
Escherichia coli
-
inhibitor shows good selectivity for peptide deformylase over several endoproteases including matrix metalloproteases, however it shows only weak antibacterial activity. IC50: 0.00031 mM
0.027
2-(5-chloro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetohydrazide
Escherichia coli
-
IC50: 0.027 mM
0.00087
2-(5-fluoro-2,2-dioxido-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00087 mM
0.00087
2-(5-fluoro-2-oxo-1,4-dihydroquinazolin-3(2H)-yl)-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00087 mM
0.0076
2-butyl-5,7-dimethyl-3-[2''-(1H-tetrazol-5-ylmethyl)-[1,1',4',1'']terphenyl-4-yl]-3H-imidazo[4,5-b]pyridine
Escherichia coli
-
belongs to a class of angiotensin II receptor antagonists, potent inhibitor, IC50: 0.0076 mM
0.00013
2-[2,2-dioxido-5-(trifluoromethyl)-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl]-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00013 mM
0.00029
2-[5-chloro-2,2-dioxido-1-(3-phenylpropyl)-1,4-dihydro-3H-2,1,3-benzothiadiazin-3-yl]-N-hydroxyacetamide
Escherichia coli
-
IC50: 0.00029 mM
0.0995
3-(5-((4H-1,2,4-triazol-4-yl)amino)-1,3,4-thiadiazol-2-yl)-4-hydroxy benzenesulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.4819
3-(5-((furan-2-ylmethyl)amino)-1,3,4-thiadiazole-2-yl)-4-hydroxybenzenesulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.2753
3-(5-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]-4H-1,2,4-triazol-3-yl)-4-hydroxybenzenesulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.0342
3-[5'-benzyl-2'-(1H-tetrazol-5-yl)-biphenyl-4-yl]-2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridine
Escherichia coli
-
potent inhibitor, IC50: 0.0342 mM, the acidic moiety forms direct ionic interactions with active site metal cation
0.3043
4-((5-(3,4-dimethoxyphenyl)-1,3,4-thiadiazol-2-yl)amino)-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
Escherichia coli
-
pH and temperature not specified in the publication
0.1035
4-hydroxy-3-(5-((5-methylisoxazol-3-yl)amino)-1,3,4-thiadiazol-2-yl)benzenesulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.1279
4-hydroxy-3-(5-[(4-methylpyridin-2-yl)amino]-4H-1,2,4-triazol-3-yl)benzenesulfonic acid
Escherichia coli
-
pH and temperature not specified in the publication
0.1725
5-(3,4-dimethoxyphenyl)-N-(4-methylpyridine-2-yl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0972
5-(3,4-dimethoxyphenyl)-N-(4H-1,2,4-triazol-4-yl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.2743
5-(3,4-dimethoxyphenyl)-N-(furan-2-ylmethyl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0039
5-chloro-2-propyl-3-[2''-(1H-tetrazol-5-ylmethyl)-[1,1',4',1'']terphenyl-4-yl]-3H-imidazo[4,5-b]pyridine
Escherichia coli
-
belongs to a broad class of angiotensin II receptor antagonists, potent competitive inhibitor, IC50: 0.0039 mM, the acidic moiety forms direct ionic interactions with active site metal cation
0.015
butyl {[4'-(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)-5-(2-methylbutan-2-yl)biphenyl-2-yl]sulfonyl}carbamate
Escherichia coli
-
competitive inhibition, IC50: 0.015 mM, the acidic moiety forms direct ionic interactions with active site metal cation
0.0165
N-(4-((Z)-phenyldiazenyl) phenyl)-5-((Z)-styryl)-1,3,4-thiadiazol-2-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.0915
N-(5-(3,4-dimethoxy phenyl)-1,3,4-thiadiazol-2-yl)-5-methylisoxazol-3-amine
Escherichia coli
-
pH and temperature not specified in the publication
0.00115
N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
Escherichia coli
-
i.e. SB 543668, IC50: 0.00115 mM
0.00016
N-formyl-N-hydroxy-3-phenylpropylamine
Escherichia coli
-
i.e. SB 485345, IC50: 0.00016 mM
0.0029
N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
Escherichia coli
-
IC50: 0.0029 mM
0.00023
N-hydroxy-2-[2-oxo-5-(trifluoromethyl)-1,4-dihydroquinazolin-3(2H)-yl]acetamide
Escherichia coli
-
IC50: 0.00023 mM
0.0028
N-hydroxy-N-[3-(6-methylpyridine-2-yl)propyl]formamide
Escherichia coli
-
i.e. SB 505684, IC50: 0.0028 mM
0.000008
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
Escherichia coli
pH and temperature not specified in the publication
0.000017
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
0.000037
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
Escherichia coli
pH 7.5, 37°C, recombinant enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
229
recombinant wild-type enzyme, cell-free extract from overexpressing cell culture, pH 7.2, 30°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.4
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
increasing activity by addition of Ni2+ or Mn2+ ions to the culture medium
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
the enzyme interacts directly with the ribosome via its C-terminal extension. The enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. The interaction of the enzyme with the ribosome enhances cell viability
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview
physiological function
physiological function
-
PDF plays a critical role in mediating the maturation process of the nascent polypeptides partly due to the necessity of removing the N-formyl group to render nascent polypeptides available for cleavage of the N-terminal methionine residue by methionine amino peptidase
additional information
evolution
PDFs of all Gram-negative bacteria, some Gram-positive bacteria, and all eukaryotes fall systematically into type I class. The type II PDFs are found in Gram-positive bacteria (with low C+G content) and mycoplasma. The def genes from Escherichia coli and Pseudomonas aeruginosa encode type I PDFs, and those from Staphylococcus aureus and Bacillus stearothermophilus encode type II PDFs
physiological function
PDF is an essential and highly conserved enzyme that functions in protein maturation by removing the N-formyl group from the methionine of nascently synthesized polypeptides
physiological function
peptide deformylases catalyze the removal of the formyl group from the N-terminal methionine residue in nascent polypeptide chains in prokaryotes
physiological function
peptide deformylase (PDF) is a metalloenzyme and responsible for catalyzing the removal of the N-formyl group from N-terminal methionine following translation. Removal of the formyl group from polypeptide by PDF is a necessary activity for prokaryotic cell viability. This activity is not believed to be important in eukaryotic cells until recently, because nuclear encoded proteins are not N-formylated. But in eukaryotes, mitochondrial protein synthesis may also involve the formylation and deformylation process
physiological function
peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins
physiological function
the metalloenzyme peptide deformylase (PDF) plays a crucial role in the biosynthesis of proteins by eubacteria, making the enzyme a promising target for antibacterial agents. In a reaction catalyzed by an Fe2+ coordination complex in the enzyme active site, PDF cleaves a formyl group from the N-terminus of nascent eubacterial proteins
additional information
proposed mechanism for the N-terminal deformylation reaction catalyzed by PDF, with active site residues, overview. The catallytic triad is formed by Cys90, His132, and His136. Aanalysis of activation and reaction free energies for deformylation
additional information
proposed molecular catalytic mechanism of PDF, overview. The active site of PDF proteins contains three substrate binding pockets along with the metal binding site. These pockets are referred to as S1', S2', and S3' pockets and corresponding positions on substrate or inhibitors are referred to as P1', P2', and P3'
additional information
Vibrio parahaemolyticus phage Vp16T and Escherichia coli PDFs display an identical substrate binding mode
additional information
-
Vibrio parahaemolyticus phage Vp16T and Escherichia coli PDFs display an identical substrate binding mode
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
19000
19200
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
monomer
additional information
additional information
comparison of PDF structures from Escherichia coli (PDB ID 1BS7), Staphylococcus aureus (PDB ID 2AI9), Plasmodium falciparum (PBD ID 1BS8), and Homo sapiens (PBD ID 3G5K), overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PDF of Escherichia coli with Ni2+ replacing the native Fe2+, hanging drop vapour diffusion method, using 20.5% (w/v) PEG 4000, 0.1 M sodium acetate, pH 4.0
crystallographic analysis of the complex between the ribosome-interacting helix of the enzyme and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains
-
Fe2+-, Ni2+- and Zn2+-bound enzyme, Met-Ala-Ser-tripeptide bound to the substrate binding-site
-
Fe2+-, Ni2+- and Zn2+-bound forms, hanging and sitting drop vapour diffusion techniques
-
structure of the catalytically active enzyme in the nickel-bound form at 2.5-A resolution and at 1.9-A resolution in complex with the competitive inhibitor polyethylene glycol molecule
-
vapour diffusion method. Crystallization of protein and protein-inhibitor complexes with N-formyl-H-hydroxy-3-phenylpropylamine, N-hydroxy-N-[3-(6-methyl pyridine-2-yl)propyl] formamide or N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C129A
-
turnover-number is 86% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.3fold higher than the Km-value of the wild-type enzyme
E133D
-
modest reduction in activity, less than 10fold for most of the substrates tested
E88F
-
turnover-number is 0.36% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.1fold higher than the Km-value of the wild-type enzyme
I128A
-
Km-value for N-formyl-Met-Ala is 8.4fold higher than the Km-value of the wild-type enzyme
I128F
-
turnover-number is 0.13% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 37% of the Km-value of the wild-type enzyme
I128R
-
turnover-number is 0.6% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 6fold higher than the Km-value of the wild-type enzyme
I128S
-
turnover-number is 11% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.25fold higher than the Km-value of the wild-type enzyme
I130F
-
turnover-number is 58% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 77% of the Km-value of the wild-type enzyme
I44F
-
turnover-number is 3.8% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 35% of the Km-value of the wild-type enzyme
I86A
-
turnover-number is 8.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.fold higher than the Km-value of the wild-type enzyme
I86F
-
turnover-number is 3.3% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 65% of the Km-value of the wild-type enzyme
L125A
-
turnover-number is 2.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 3fold higher than the Km-value of the wild-type enzyme
L125W
-
turnover-number is 0.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.9fold higher than the Km-value of the wild-type enzyme
L126F
-
turnover-number is 113% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.5fold higher than the Km-value of the wild-type enzyme
L91E
-
the ratio of turnover number to Km-value for the substrate formyl-Met-Leu-p-nitroanilide is decreased 10fold
additional information
additional information
fusion of the enzyme to an octaglutamate tag-deformylation activity and stability of the engineered enzyme are similar to those of the wild-type
additional information
-
fusion of the enzyme to an octaglutamate tag-deformylation activity and stability of the engineered enzyme are similar to those of the wild-type
additional information
generation of several chimeric enzyme mutants PDFS with various length of their C-domain constructed from Vp16 PDF and Escherichia coli PDF, and complementation of Escherichia coli strain PAL421Tr which is deficient for enzyme PDF, substrate specificity analysis and comparison, overview
additional information
-
construction of a C-terminal 21 amino acid truncated enzyme
additional information
-
C-terminally histidine-tagged, PDF-H6, is well expressed and has identical physical and catalytic properties as the wild-type enzyme, N-terminally histidine-tagged enzyme shows drastically reduced catalytic activity
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+)
68
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) and inhibitor actinonin
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
denaturation with guanidinium hydrochloride, protein 1 unfolds at more than 3 M, protein 2 unfolds at 1.7 M
-
Ni2+-bound enzyme fully stable, additional stabilization during purification by catalase
-
the enzyme undergoes slow denaturation in the presence of varying concentrations of GdmCl. Abrupt reversal of the unfolding pathway is observed at low to moderate concentrations of the denaturant, but not at high concentration
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
N,N-dimethylformamide
inactivates the enzyme at 10%, DMSO and methanol at about 40%
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
instable towards oxidation due to the oxidation of the metal ligating cysteine residue
666015
active peptide deformylase has an Fe2+ ion in the active site, which reacts readily with oxygen. To obtain a stable variant, Fe ist often substituted with Zn.
-
674160
Fe2+-containing peptide deformylase is very unstable because of its sensibility toward environmental oxygen
-
675609
presence of H2O2 and O2 leads to inactivation, enzymatic exclusion of O2 renders the deformylase highly stable. Zn2+-bound enzyme form is not sensitive to oxidation
-
393807
sensitive to intracellular reactive oxygen
-
393798, 393799, 393800, 393804, 393807
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Poros 20 MC column chromatography and Poros 20 HQ column chromatography
recombinant enzyme 8.2fold by Met-Lys affinity chromatography, recombinant enzyme fused to an octaglutamate tag 5-5.5fold by two different methods of anion exchange chromatography, ultrafiltration, and gel filtration, deformylation activity and stability of the engineered enzyme are similar to those of the wild-type
recombinant enzyme from Escherichia coli strains PAL421Tr and Rosetta2(DE3)pLysS by cation exchange chromatography and gel filtration or dialysis, in presence of Ni2+
based of one affinity chromatography step, 200 mg of pure Escherichia coli peptide deformylase, EcPDF, were yielded from 1l of culture
-
to homogeneity, recombinant C-terminal truncated enzyme, preliminary Zn2+-bound, 10fold more active than Co2+-bound enzyme
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene def, recombinant expression of the enzyme fused to an octaglutamate tag using expression vector pBAD/Myc-His-DEST in Escherichia coli TOP10 cells and strain JM109
recombinant expression in Escherichia coli strains PAL421Tr (PDF knockout) and Rosetta2(DE3)pLysS
Escherichia coli chromosomal def gene is cloned into the pLysS expression plasmid for co-transformation with pET-based expression vectors
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
medicine
synthesis
the enzyme is an attractive candidate for the biocatalytic deprotection of formylated peptides that are used in chemoenzymatic peptide synthesis
analysis
-
novel class of N-formylated peptides for routine kinetic characterization and for screening PDF inhibitors
biotechnology
-
to avoid incomplete deformylation for proteins overexressed in Escherichia coli
medicine
drug development
potential target or the development of new antibacterial agents
drug development
-
potential target or the development of new antibacterial agents
drug development
peptide deformylase (PDF) is considered an excellent target to develop antibiotics
drug development
the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview
drug development
the enzyme is an important antibacterial drug target
medicine
antibacterial activity against clinically significant Gram-positive and Gram-negative pathogens
medicine
peptide deformylase represents a target for the discovery of broad spectrum antibacterial drugs
medicine
peptide deformylase becomes a target for the design of new antibiotics
medicine
-
possible target for new broad spectrum antimicrobial agents
medicine
-
peptide deformylase may be a potential target for designing new antibiotics
medicine
-
peptide deformylase is a therapeutic target for antibacterial drug discovery
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Giglione, C.; Pierre, M.; Meinnel, T.
Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents
Mol. Microbiol.
36
1197-1205
2000
Arabidopsis thaliana, Geobacillus stearothermophilus, Escherichia coli, Enterococcus faecalis, Solanum lycopersicum, Staphylococcus aureus, no activity in Caenorhabditis elegans, no activity in Saccharomyces cerevisiae, Plasmodium falciparum, Trypanosoma sp.
Green, B.G.; Toney, J.H.; Kozarich, J.W.; Grant, S.K.
Inhibition of bacterial peptide deformylase by biaryl acid analogs
Arch. Biochem. Biophys.
375
355-358
2000
Escherichia coli
Rajagopalan, P.T.R.; Grimme, S.; Pei, D.
Characterization of Cobalt(II)-substituted peptide deformylase: Function of the metal ion and the catalytic residue Glu-133
Biochemistry
39
779-790
2000
Escherichia coli
Hu, Y.J.; Wie, Y.; Zhou, Y.; Rajagopalan, P.T.R.; Pei, D.
Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library
Biochemistry
38
643-650
1999
Escherichia coli
Becker, A.; Schlichting, I.; Kabsch, W.; Groche, D.; Schultz, S.; Wagner, A.F.V.
Iron center, substrate recognition and mechanism of peptide deformylase
Nature Struct. Biol.
5
1053-1058
1998
Escherichia coli
Ragusa, S.; Blanquet, S.; Meinnel, T.
Control of peptide deformylase activity by metal cations
J. Mol. Biol.
280
515-523
1998
Geobacillus stearothermophilus, Escherichia coli, Thermus thermophilus
Groche, D.; Becker, A.; Schlichting, I.; Kabsch, W.; Schultz, S.; Wagner, A.F.V.
Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site
Biochem. Biophys. Res. Commun.
246
342-346
1998
Escherichia coli
Rajagopalan, P.T.R.; Datta, A.; Pei, D.
Purification, characterization, and inhibition of peptide deformylase from Escherichia coli
Biochemistry
36
13910-13918
1997
Escherichia coli
Meinnel, T.; Blanquett, S.
Enzymatic properties of Escherichia coli peptide deformylase
J. Bacteriol.
177
1883-1887
1995
Escherichia coli
Rajagopalan, P.T.R.; Pei, D.
Oxygen-mediated inactivation of peptide deformylase
J. Biol. Chem.
273
22305-22310
1998
Escherichia coli
Grant, S.K.; Green, B.G.; Kozarich, J.W.
Inhibition and structure-activity studies of methionine hydroxamic acid derivatives with bacterial peptide deformylase
Bioorg. Chem.
29
211-222
2001
Escherichia coli
Serero, A.; Giglione, C.; Meinnel, T.
Distinctive features of the two classes of eukaryotic peptide deformylases
J. Mol. Biol.
314
695-708
2001
Arabidopsis thaliana, Escherichia coli, Solanum lycopersicum
Apfel, C.; Banner, D.W.; Bur, D.; Dietz, M.; Hirata, T.; Hubschwerlen, C.; Locher, H.; Page, M.G.P.; Pirson, W.; Rosse, G.; Specklin, J.L.
Hydroxyamic acid derivates as potent peptide deformylase inhibitors and antibacterial agents
J. Med. Chem.
43
2324-2331
2000
Escherichia coli
Guo, X.C.; Rajagopalan, P.T.R.; Pei, D.
A direct spectrophotometric assay for peptide deformylase
Anal. Biochem.
273
298-304
1999
Escherichia coli
Rajagopalan, P.T.R.; Yu, X.C.; Pei, D.
Peptide deformylase: A new type of mononuclear iron protein
J. Am. Chem. Soc.
119
12418-12419
1997
Escherichia coli, Haemophilus influenzae
-
Chan, M.K.; Gong, W.; Rajagopalan, P.T.R.; Hao, B.; Tsai, C.M.; Pei, D.
Crystal structure of the Escherichia coli peptide deformylase
Biochemistry
36
13904-13909
1997
Staphylococcus aureus, Escherichia coli (P0A6K3), Escherichia coli
Ragusa, S.; Mouchet, P.; Lazennec, C.; Dive, V.; Meinnel, T.
Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin
J. Mol. Biol.
289
1445-1457
1999
Escherichia coli
Becker, A.; Schlichting, I.; Kabsch, W.; Schultz, S.; Volker Wagner, A.F.
Structure of peptide deformylase and identification of the substrate binding site
J. Biol. Chem.
273
11413-11416
1998
Escherichia coli
Durand, D.J.; Green, B.G.; OConnell, J.F.; Grant, S.K.
Peptide aldehyde inhibitors of bacterial peptide deformylase
Arch. Biochem. Biophys.
367
297-302
1999
Bacillus subtilis, Escherichia coli
Meinnel, T.; Blanquet, S.; Dardel, F.
A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase
J. Mol. Biol.
262
375-386
1996
Escherichia coli (P0A6K3), Escherichia coli
Nguyen, K.T.; Hu, X.; Colton, C.; Chakrabarti, R.; Zhu, M.X.; Pei, D.
Characterization of a human peptide deformylase: implications for antibacterial drug design
Biochemistry
42
9952-9958
2003
Escherichia coli, Homo sapiens
Apfel, C.; Banner, D.W.; Bur, D.; Dietz, M.; Hubschwerlen, C.; Locher, H.; Marlin, F.; Masciadri, R.; Pirson, W.; Stalder, H.
2-(2-Oxo-1,4-dihydro-2H-quinazolin-3-yl)- and 2-(2,2-dioxo-1,4-dihydro-2H-2lambda6-benzo[1,2,6]thiadiazin-3-yl)-N-hydrox y-acetamides as potent and selective peptide deformylase inhibitors
J. Med. Chem.
44
1847-1852
2001
Escherichia coli
Smith, K.J.; Petit, C.M.; Aubart, K.; Smyth, M.; McManus, E.; Jones, J.; Fosberry, A.; Lewis, C.; Lonetto, M.; Christensen, S.B.
Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species
Protein Sci.
12
349-360
2003
Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Staphylococcus aureus
Guilloteau, J.P.; Mathieu, M.; Giglione, C.; Blanc, V.; Dupuy, A.; Chevrier, M.; Gil, P.; Famechon, A.; Meinnel, T.; Mikol, V.
The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents
J. Mol. Biol.
320
951-962
2002
Geobacillus stearothermophilus (O31410), Escherichia coli (P0A6K3), Staphylococcus aureus (P68826), Staphylococcus aureus, Pseudomonas aeruginosa (Q9I7A8), Pseudomonas aeruginosa, Staphylococcus aureus RN4220 (P68826)
Kreusch, A.; Spraggon, G.; Lee, C.C.; Klock, H.; McMullan, D.; Ng, K.; Shin, T.; Vincent, J.; Warner, I.; Ericson, C.; Lesley, S.A.
Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
J. Mol. Biol.
330
309-321
2003
Escherichia coli (P0A6K3), Escherichia coli, Plasmodium falciparum, Pseudomonas aeruginosa (Q9I7A8), Pseudomonas aeruginosa, Staphylococcus aureus (P68826), Staphylococcus aureus, Staphylococcus aureus ATCC 2913 (P68826), Streptococcus pneumoniae (Q9F2F0), Streptococcus pneumoniae, Thermotoga maritima (P96113), Thermotoga maritima, Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589 (P96113)
Cali, P.; Naerum, L.; Mukhija, S.; Hjelmencrantz, A.
Isoxazole-3-hydroxamic acid derivatives as peptide deformylase inhibitors and potential antibacterial agents
Bioorg. Med. Chem. Lett.
14
5997-6000
2004
Staphylococcus aureus, Escherichia coli (P0A6K3)
Chae, P.S.; Kim, M.; Jeung, C.; Lee, S.D.; Park, H.; Lee, S.; Suh, J.
Peptide-cleaving catalyst selective for peptide deformylase
J. Am. Chem. Soc.
127
2396-2397
2005
Escherichia coli
Hu, X.; Nguyen, K.T.; Jiang, V.C.; Lofland, D.; Moser, H.E.; Pei, D.
Macrocyclic inhibitors for peptide deformylase: a structure-activity relationship study of the ring size
J. Med. Chem.
47
4941-4949
2004
Escherichia coli (P0A6K3)
Sonke, T.; Kaptein, B.; Wagner, A.F.; Quaedflieg, P.J.; Schultz, S.; Ernste, S.; Schepers, A.; Mommers, J.H.; Broxterman, Q.B.
Peptide deformylase as biocatalyst for the synthesis of enantiomerically pure amino acid derivatives
J. Mol. Catal. B
29
265-277
2004
Escherichia coli
-
Leopoldini, M.; Russo, N.; Toscano, M.
Role of the metal ion in formyl-peptide bond hydrolysis by a peptide deformylase active site model
J. Phys. Chem. B
110
1063-1072
2006
Escherichia coli
Tang, J.; Hernandez, G.; LeMaster, D.M.
Increased peptide deformylase activity for N-formylmethionine processing of proteins overexpressed in Escherichia coli: application to homogeneous rubredoxin production
Protein Expr. Purif.
36
100-105
2004
Escherichia coli
Bingel-Erlenmeyer, R.; Kohler, R.; Kramer, G.; Sandikci, A.; Antolic, S.; Maier, T.; Schaffitzel, C.; Wiedmann, B.; Bukau, B.; Ban, N.
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing
Nature
452
108-111
2008
Escherichia coli
Shen, G.; Zhu, J.; Simpson, A.M.; Pei, D.
Design and synthesis of macrocyclic peptidyl hydroxamates as peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
18
3060-3063
2008
Escherichia coli
Chikhi, A.; Bensegueni, A.; Boulahrouf, A.; Bencharif, M.
Theoretical study of Escherichia coli peptide deformylase inhibition by several drugs
In Silico Biol.
6
459-466
2006
Escherichia coli (P0A6K3), Escherichia coli
Boularot, A.; Giglione, C.; Petit, S.; Duroc, Y.; Alves de Sousa, R.; Larue, V.; Cresteil, T.; Dardel, F.; Artaud, I.; Meinnel, T.
Discovery and refinement of a new structural class of potent peptide deformylase inhibitors
J. Med. Chem.
50
10-20
2007
Arabidopsis thaliana, Arabidopsis thaliana (Q9FUZ2), Arabidopsis thaliana (Q9FV53), Bacillus subtilis, Escherichia coli, Homo sapiens
Xiao, C.; Zhang, Y.
Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study
J. Phys. Chem. B
111
6229-6235
2007
Escherichia coli (P0A6K3)
Wu, X.H.; Quan, J.M.; Wu, Y.D.
Theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
J. Phys. Chem. B
111
6236-6244
2007
Escherichia coli (P0A6K3), Escherichia coli
Berg, A.K.; Manokaran, S.; Eiler, D.; Kooren, J.; Mallik, S.; Srivastava, D.K.
Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase
Protein Sci.
17
11-15
2008
Escherichia coli
Berg, A.K.; Srivastava, D.K.
Delineation of alternative conformational states in Escherichia coli peptide deformylase via thermodynamic studies for the binding of actinonin
Biochemistry
48
1584-1594
2009
Escherichia coli (P0A6K3), Escherichia coli
Dong, M.; Liu, H.
Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study
J. Phys. Chem. B
112
10280-10290
2008
Escherichia coli (P0A6K3), Escherichia coli
Amero, C.D.; Byerly, D.W.; McElroy, C.A.; Simmons, A.; Foster, M.P.
Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase
Biochemistry
48
7595-7607
2009
Escherichia coli (P0A6K3), Escherichia coli
Berg, A.K.; Yu, Q.; Qian, S.Y.; Haldar, M.K.; Srivastava, D.K.
Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase
Biochim. Biophys. Acta
1804
704-713
2010
Escherichia coli (P0A6K3), Escherichia coli
Shi, W.; Duan, Y.; Qian, Y.; Li, M.; Yang, L.; Hu, W.
Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives as novel peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
20
3592-3595
2010
Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis
Sharma, A.; Khuller, G.K.; Sharma, S.
Peptide deformylase--a promising therapeutic target for tuberculosis and antibacterial drug discovery
Expert Opin. Ther. Targets
13
753-765
2009
Bacillus subtilis, Bacteroides fragilis, Enterobacter cloacae, Enterococcus sp., Escherichia coli, Homo sapiens, Klebsiella pneumoniae, Moraxella catarrhalis, Mycobacterium tuberculosis, Mycobacterium tuberculosis variant bovis, Neisseria gonorrhoeae, Plasmodium falciparum, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Stenotrophomonas maltophilia, Streptococcus pneumoniae
Yen, N.T.; Bogdanovic, X.; Palm, G.J.; Kuehl, O.; Hinrichs, W.
Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres
J. Biol. Inorg. Chem.
15
195-201
2009
Escherichia coli (P0A6K3), Escherichia coli
Chikhi, A.; Bensegueni, A.
In silico study of the selective inhibition of bacterial peptide deformylases by several drugs
J. Proteomics Bioinform.
3
61-65
2010
Escherichia coli (P0A6K3), Bacillus cereus (Q819K2), Arabidopsis thaliana (Q9FUZ2), Homo sapiens (Q9HBH1)
-
Yang, S.; Shi, W.; Xing, D.; Zhao, Z.; Lv, F.; Yang, L.; Yang, Y.; Hu, W.
Synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria
Eur. J. Med. Chem.
86
133-152
2014
Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis
Di Toma, C.; Sonke, T.; Quaedflieg, P.J.; Volker Wagner, A.F.; Janssen, D.B.
Purification and use of E. coli peptide deformylase for peptide deprotection in chemoenzymatic peptide synthesis
Protein Expr. Purif.
89
73-79
2013
Escherichia coli (P0A6K3), Escherichia coli
Grzela, R.; Nusbaum, J.; Fieulaine, S.; Lavecchia, F.; Desmadril, M.; Nhiri, N.; Van Dorsselaer, A.; Cianferani, S.; Jacquet, E.; Meinnel, T.; Giglione, C.
Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts
Biochim. Biophys. Acta
1866
348-355
2018
Escherichia coli (P0A6K3), Escherichia coli, Vibrio phage VP16T (Q6VT21)
Khan, F.A.K.; Jadhav, K.S.; Patil, R.H.; Shinde, D.B.; Arote, R.B.; Sangshetti, J.N.
Biphenyl tetrazole-thiazolidinediones as novel bacterial peptide deformylase inhibitors synthesis, biological evaluations and molecular docking study
Biomed. Pharmacother.
83
1146-1153
2016
Escherichia coli (P0A6K3), Escherichia coli
Khan, F.A.; Patil, R.H.; Shinde, D.B.; Sangshetti, J.N.
Bacterial peptide deformylase inhibition of cyano substituted biaryl analogs synthesis, in vitro biological evaluation, molecular docking study and in silico ADME prediction
Bioorg. Med. Chem.
24
3456-3463
2016
Escherichia coli (P0A6K3), Escherichia coli
Lv, F.; Chen, C.; Tang, Y.; Wei, J.; Zhu, T.; Hu, W.
New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment
Bioorg. Med. Chem. Lett.
26
3714-3718
2016
Escherichia coli (P0A6K3), Staphylococcus aureus (P68826)
Khan, F.A.; Patil, R.H.; Shinde, D.B.; Sangshetti, J.N.
Design and synthesis of 4-((5-benzylidene-2,4-dioxothiazolidin-3-yl)methyl)biphenyl-2-carbonitrile analogs as bacterial peptide deformylase inhibitors
Chem. Biol. Drug Des.
88
938-944
2016
Escherichia coli (P0A6K3), Escherichia coli
Sangshetti, J.; Khan, F.; Shinde, D.
Peptide deformylase a new target in antibacterial, antimalarial and anticancer drug discovery
Curr. Med. Chem.
22
214-236
2015
Bacillus subtilis (P94462), Bacillus subtilis 168 (P94462), Escherichia coli (P0A6K3), Haemophilus influenzae (P44786), Haemophilus influenzae ATCC 51907 (P44786), Haemophilus influenzae DSM 11121 (P44786), Haemophilus influenzae KW20 (P44786), Haemophilus influenzae RD (P44786), Helicobacter pylori (P56419), Helicobacter pylori 26695 (P56419), Helicobacter pylori ATCC 700392 (P56419), Homo sapiens (Q9HBH1), Homo sapiens, Mycobacterium tuberculosis (P9WIJ3), Mycobacterium tuberculosis ATCC 25618 (P9WIJ3), Mycobacterium tuberculosis H37Rv (P9WIJ3), Plasmodium falciparum (Q8I372), Plasmodium falciparum isolate 3D7 (Q8I372), Staphylococcus aureus (P68826)
Gao, J.; Liang, L.; Zhu, Y.; Qiu, S.; Wang, T.; Zhang, L.
Ligand and structure-based approaches for the identification of peptide deformylase inhibitors as antibacterial drugs
Int. J. Mol. Sci.
17
E1141
2016
Escherichia coli (P0A6K3), Escherichia coli
Vadivelu, A.; Gopal, V.; Uma Maheswara Reddy, C.
Molecular docking studies of 1,3,4-thiadiazoles as novel peptide deformylase inhibitors as potential antibacterial agents
Int. J. Pharm. Sci. Rev. Res.
31
58-62
2015
Escherichia coli, Escherichia coli ATCC 11775
-
Fieulaine, S.; Alves de Sousa, R.; Maigre, L.; Hamiche, K.; Alimi, M.; Bolla, J.M.; Taleb, A.; Denis, A.; Pages, J.M.; Artaud, I.; Meinnel, T.; Giglione, C.
A unique peptide deformylase platform to rationally design and challenge novel active compounds
Sci. Rep.
6
35429
2016
Escherichia coli (P0A6K3), Streptococcus agalactiae (Q8E378), Streptococcus agalactiae, Arabidopsis thaliana (Q9FUZ2), Streptococcus agalactiae NEM316 (Q8E378)
Grzela, R.; Nusbaum, J.; Fieulaine, S.; Lavecchia, F.; Bienvenut, W.V.; Dian, C.; Meinnel, T.; Giglione, C.
The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation
Sci. Rep.
7
11041
2017
Escherichia coli (P0A6K3), Vibrio phage VP16T (Q6VT21)
Fell, J.; Steele, D.; Hatcher, T.I.; Gherman, B.
Electronic effects on the reaction mechanism of the metalloenzyme peptide deformylase
Theoret. Chem. Accounts
134
71
2015
Escherichia coli (P0A6K3)
-
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