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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Staphylococcus aureus and UniProt Accession P68826
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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: Staphylococcus aureus
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
deformylase, peptide N-formylmethionine
-
-
-
-
hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
PDF
Polypeptide deformylase
-
-
-
-
PDF
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
N-formyl-L-methionine polypeptide + H2O
formate + methionine-polypeptide
-
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
-
?
formyl-Met-Ala-Ser + H2O
formate + Met-Ala-Ser
-
-
-
-
?
formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
-
-
-
-
?
N-formyl-L-methionine polypeptide + H2O
formate + methionine-polypeptide
-
-
-
-
?
additional information
?
-
-
peptide deformylase is responsible for the removal of the N-formyl group from the terminal methionine residue in bacterial protein synthesis
-
-
?
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
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
-
?
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
N-formyl-L-methionine polypeptide + H2O
formate + methionine-polypeptide
-
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
-
-
-
-
?
N-formyl-L-methionine polypeptide + H2O
formate + methionine-polypeptide
-
-
-
-
?
additional information
?
-
-
peptide deformylase is responsible for the removal of the N-formyl group from the terminal methionine residue in bacterial protein synthesis
-
-
?
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
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Fe2+
Ni2+
Fe2+
Ni2+
-
the imidazole ring of histidine can combine with a metal ion such as nickel. The activity of the iron form of the enzyme is higher than the nickel form
Zn2+
additional information
Co2+
can replace Fe2+ without loss of activity, enhances stability
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
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
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Fe2+
-
the imidazole ring of histidine can combine with a metal ion such as iron. The activity of the iron form of the enzyme is higher than the nickel form
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
(2E)-3-(2,5-dihydroxyphenyl)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one
-
(2R)-N4-hydroxy-N1-[(2R)-1-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]-2-pentylbutanediamide
-
(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)-2-[[(9H-fluoren-9-ylmethoxy)carbonyl]amino]pent-4-ynoic acid
-
(2S,3R,4S,5R,6R)-2-[(5-bromo-1H-indol-3-yl)oxy]-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol
-
(2S,3R,4S,5S,6R)-2-[(5-bromo-6-chloro-1H-indol-3-yl)oxy]-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol
-
(2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide
active against Staphylococcus aureus strains
(4S)-N-[3-chloro-2-(morpholin-4-yl)phenyl]-3-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-1,3-oxazolidine-4-carboxamide
active against Staphylococcus aureus and Streptomyces strains
(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
-
1-[(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl]-4-methylidene-N-(5-methyl-1,3-thiazol-2-yl)-L-prolinamide
active against Staphylococcus aureus strains
1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide
active against Staphylococcus aureus strains
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2,2-dimethylpropanoyl)-L-prolinamide
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2-methylpropanoyl)-L-prolinamide
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(3-methylbutanoyl)-L-prolinamide
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(cyclopropylcarbonyl)-L-prolinamide
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methoxyacetyl)-L-prolinamide
-
2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide
-
2-(4-benzyl-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)-N-oxoacetamide
-
2-(4-[2-[(2,5-difluorophenyl)amino]-2-oxoethyl]-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)-N-oxoacetamide
-
2-amino-N-[(1S,2S)-1-hydroxy-1-phenylpropan-2-yl]-N-methylacetamide
-
2-[2-[(2-hydroxyethyl)amino]-1H-benzimidazol-1-yl]-1-phenylethanone
-
2-[4-(3,3-dimethyl-2-oxobutyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
-
2-[4-(3-methylbutyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
-
2-[4-(cyclobutylmethyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
-
2-[[formyl(hydroxy)amino]methyl]-N-[(5-methoxy-1H-benzimidazol-2-yl)methyl]hexanamide
potently active versus Staphylococcus aureus strains and the Ni-PDF enzyme
3-methoxy-7-methyl-1,3-dihydro-2-benzofuran-4,5,6-triol
has antibacterial activity on Staphylococcus aureus strains
4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol
has antibacterial activity on Staphylococcus aureus strains
5-[[(2-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
-
5-[[(3,4-dichlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
-
5-[[(3-chlorophenyl)sulfonyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
-
5-[[(4-methoxyphenyl)sulfonyl]methyl]-1,2-oxazole-3-carbohydrazide
-
cryptochlorogenic acid
with high score in enzyme docking analysis
drechmerin I
an antibacterial compound, isolated from the fermentation broth of Drechmeria sp. strain SYPF 8335, which is isolated from the inside root of Panax notoginseng, from Wenshan district, Yunnan province of China. Compound structure determination by mass spectrometry and 1H and 13C NMR. Molecular docking in the active site of PDF from Staphylococcus aureus through the hydrogen bonds with Try88 and Arg143. Drechmerin I displays antimicrobial activity against Bacillus subtillis with an MIC value of 0.2 mg/ml
ethyl 2-amino-6-bromo-4-(1-cyano-2-ethoxy-2-oxoethyl)-4H-chromene-3-carboxylate
-
fumimycin
isolated from the fermentation broth of Aspergillus fumisynnematus strain F746
macrolactin N
isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains
methyl 4-(2-benzylbenzoyl)-2,5-dimethyl-1H-pyrrole-3-carboxylate
-
N-(5-fluoro-1-oxidopyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
N-(benzyloxy)-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
-
N-(cyclobutylcarbamoyl)-1-[(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl]-L-prolinamide
active against Staphylococcus aureus, Haemophilus influenzae, and Streptomyces pneumoniae strains
N-(cyclobutylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
N-(cyclohexylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
N-(cyclopentylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
N-acetyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
N-benzoyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
N-hydroxy-5-([[2-(propan-2-yl)phenyl]sulfanyl]methyl)-1,2-oxazole-3-carboxamide
-
N-hydroxy-5-([[4-(trifluoromethyl)phenyl]sulfanyl]methyl)-1,2-oxazole-3-carboxamide
-
N-methoxy-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
-
N-methoxy-N-methyl-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
-
N-oxo-2-[3-oxo-4-(2-phenylethyl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
-
N-oxo-2-[3-oxo-4-(tetrahydro-2H-pyran-2-ylmethyl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
-
N-oxo-2-[3-oxo-4-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
-
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-[3-fluoro-4-(1H-pyrrol-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
active against Staphylococcus aureus and Streptomyces pneumoniae strains
(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)-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
-
-
(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-(5-methylthiazol-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)-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
-
-
1-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-4-methylidene-N,N-dimorpholin-4-yl-L-prolinamide
-
-
1-(3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl)-4-methylidene-N,N-dimorpholin-4-yl-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(2-methylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(3-methylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methoxyphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-morpholin-4-ylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-piperidin-1-ylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-pyrrolidin-1-ylphenyl)-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(1H-pyrrol-1-yl)phenyl]-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-methylpiperazin-1-yl)phenyl]-L-prolinamide
-
-
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-oxidomorpholin-4-yl)phenyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2,2-dimethylpropanoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2-methylpropanoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(3-methylbutanoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(cyclopropylcarbonyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(ethoxycarbonyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(ethylcarbamoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methoxyacetyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methoxycarbonyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methylcarbamoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(prop-2-en-1-ylcarbamoyl)-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(2-hydroxyethyl)carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(3-hydroxypropyl)carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(3-phenylpropyl)carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(cyclopentyloxy)carbonyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(propan-2-yloxy)carbonyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(tetrahydro-2H-pyran-4-yloxy)carbonyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(1H-imidazol-4-yl)ethyl]carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyrazin-2-yl)ethyl]carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-2-yl)ethyl]carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-3-yl)ethyl]carbamoyl]-L-prolinamide
-
-
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-4-yl)ethyl]carbamoyl]-L-prolinamide
-
-
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
-
-
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
-
-
analogues of actinonin
-
35 different compounds were synthesized and compared to the inhibitory activity of actinonin
-
flavimycin A
-
a dimeric 1,3-dihydroisobenzofuran, isolated from cultures of Aspergillus flavipes, structure analysis by NMR and mass spectrometry, the inhibitor exists as epimeric mixture at C-1 through fast hemiacetal-aldehyde tautomerism. The compound has antibacterial activity against Staphylococcus aureus including MRSA, with MIC values of 0.032-0.064 mg/mL
flavimycin B
-
a dimeric 1,3-dihydroisobenzofuran, isolated from cultures of Aspergillus flavipes, structure analysis by NMR and mass spectrometry, the inhibitor exists as epimeric mixture at C-1 through fast hemiacetal-aldehyde tautomerism. The compound has antibacterial activity against Staphylococcus aureus including MRSA, with MIC values of 0.032-0.064 mg/mL
isoxazole-3-hydroxamic acids
-
23 different compounds were synthesized and compared to the inhibitory activity of actinonin
-
N-((R)-2-(cyclopentylmethyl)-3-((S)-2-(morpholine-4-carbonyl)-2,5-dihydro-1H-pyrrol-1-yl)-3-oxopropyl)-N-hydroxyformamide
-
-
N-(2-[[(2S)-2-[[1,3-bis(4-fluorophenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
-
N-(2-[[(2S)-2-[[1,3-bis(4-hydroxyphenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
-
N-(2-[[(2S)-2-[[1,3-bis(5-fluoro-1-oxidopyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
-
N-(2-[[(2S)-2-[[1,3-bis(5-fluoropyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
-
N-(2-[[(2S)-2-[[1,3-bis(5-methyl-1,3-thiazol-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
-
N-(3,4-difluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-chloro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-chloro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-chloro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-fluoro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-fluoro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(3-fluoro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(4-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(4-fluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(5-fluoro-1-hydroxypyridin-1-ium-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]prolinamide
-
-
N-(5-fluoro-1-oxidopyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-(benzylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclobutylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclobutylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclohexylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclohexylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclopentylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(cyclopentylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(tert-butoxycarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-(tert-butylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-acetyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-benzoyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-carbamoyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
i.e. SB 543668, IC50: 0.0022 mM
N-formyl-N-hydroxy-3-phenylpropylamine
-
i.e. SB 485345, IC50: 0.00025 mM
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: 0.00109 mM
N-[(2-aminoethyl)carbamoyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
-
binding structure, overview
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-[(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-[(2R,4S)-2-butyl-4-[[(2-fluorophenyl)carbamoyl]amino]-5-methyl-3-oxohexyl]-N-hydroxyformamide
-
binding structure, overview
N-[(2R,4S)-2-butyl-5-methyl-4-[[(5-methylpyridin-2-yl)carbamoyl]amino]-3-oxohexyl]-N-hydroxyformamide
-
binding structure, overview
N-[(3,5-difluorophenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
-
binding structure, overview
N-[(3-amino-3-oxopropyl)carbamoyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-[(cyclobutyloxy)carbonyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-[(cyclohexyloxy)carbonyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
-
-
N-[2-(cyclopentylmethyl)-3-[(2S)-2-[(1,3-dicyclopropyltriazan-2-yl)carbonyl]-4-methylidenepyrrolidin-1-yl]-3-oxopropyl]-N-hydroxyformamide
-
-
N-[2-([(2S)-2-[(1,3-diphenyltriazan-2-yl)carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl)hexyl]-N-hydroxyformamide
-
-
N-[3-chloro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[3-fluoro-4-(1-oxidopiperidin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[3-fluoro-4-(1H-pyrrol-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[3-fluoro-4-(4-methyl-1,4-diazepan-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[3-fluoro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[3-[(2S)-2-[[1,3-bis(4-fluorophenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
-
N-[3-[(2S)-2-[[1,3-bis(5-fluoro-1-oxidopyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
-
N-[3-[(2S)-2-[[1,3-bis(5-fluoropyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
-
N-[3-[(2S)-2-[[1,3-bis(5-methyl-1,3-thiazol-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
-
-
N-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
N-[4-(4-ethylpiperazin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
-
piperidin-4-yl [1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolyl]carbamate
-
-
5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
-
5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
poor antibacterial activity
actinonin
-
actinonin does exert a significant inhibitory effect on enzyme activity in the presence of 0.25 mM substrate (complete inhibition at 10 nM)
GSK1322322
-
an enzyme inhibitor being developed for the intravenous and oral treatment of acute bacterial skin and skin structure infections of humans and hospitalized patients with community-acquired pneumonia. The compound shows good antibacterial activity against common RTI and SSSI pathogens, overview
additional information
different classes of PDF inhibitors, structures, and molecular modeling studies, overview
-
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
PDF-based virtual screening of compounds from Traditional Chinese Medicine (TCM) and discovery of antibacterial natural compounds via inhibition of peptide deformylase, MIC values, overview
-
additional information
-
PDF-based virtual screening of compounds from Traditional Chinese Medicine (TCM) and discovery of antibacterial natural compounds via inhibition of peptide deformylase, MIC values, overview
-
additional information
-
there is no significant inhibitory effect of actinonin on enzyme activity when the concentration of substrate is 4 mM
-
additional information
-
effects of inhibitors on the enzyme structure, overview
-
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
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0000849
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
-
pH 7.0, temperature not specified in the publication
0.0000351
N-[(2R,4S)-2-butyl-4-[[(2-fluorophenyl)carbamoyl]amino]-5-methyl-3-oxohexyl]-N-hydroxyformamide
-
pH 7.0, temperature not specified in the publication
0.0000112
N-[(2R,4S)-2-butyl-5-methyl-4-[[(5-methylpyridin-2-yl)carbamoyl]amino]-3-oxohexyl]-N-hydroxyformamide
-
pH 7.0, temperature not specified in the publication
0.0000524
N-[(3,5-difluorophenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
-
pH 7.0, temperature not specified in the publication
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000002
(2R)-N4-hydroxy-N1-[(2R)-1-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]-2-pentylbutanediamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000012
2-(4-benzyl-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000058
2-(4-[2-[(2,5-difluorophenyl)amino]-2-oxoethyl]-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.05
2-(biphenyl-4-yl)-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.00005
2-[4-(3,3-dimethyl-2-oxobutyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000005
2-[4-(3-methylbutyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000041
2-[4-(cyclobutylmethyl)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-oxoacetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0025
3-methoxy-7-methyl-1,3-dihydro-2-benzofuran-4,5,6-triol
Staphylococcus aureus
pH and temperature not specified in the publication
0.0036
4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol
Staphylococcus aureus
pH and temperature not specified in the publication
0.0038
5-[[(2-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.002
5-[[(3,4-dichlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0017
5-[[(3-chlorophenyl)sulfonyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0065
5-[[(4-methoxyphenyl)sulfonyl]methyl]-1,2-oxazole-3-carbohydrazide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0041
fumimycin
Staphylococcus aureus
pH and temperature not specified in the publication
0.0075
macrolactin N
Staphylococcus aureus
pH and temperature not specified in the publication
0.00023
N-(benzyloxy)-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000005
N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0076
N-hydroxy-5-([[2-(propan-2-yl)phenyl]sulfanyl]methyl)-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0087
N-hydroxy-5-([[4-(trifluoromethyl)phenyl]sulfanyl]methyl)-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000074
N-methoxy-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.002
N-methoxy-N-methyl-2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl)acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000005
N-oxo-2-[3-oxo-4-(2-phenylethyl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.000018
N-oxo-2-[3-oxo-4-(tetrahydro-2H-pyran-2-ylmethyl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0004
N-oxo-2-[3-oxo-4-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.1
naphthalen-1-yl[[3-(trifluoromethyl)benzyl]amino]acetic acid
Staphylococcus aureus
pH and temperature not specified in the publication
0.00001
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2,2-dimethylpropanoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000005
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(2-methylpropanoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000004
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(3-methylbutanoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000023
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(cyclopropylcarbonyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000022
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(ethoxycarbonyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000002
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(ethylcarbamoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000008
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methoxyacetyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000045
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methoxycarbonyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000021
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(methylcarbamoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.00001
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-(prop-2-en-1-ylcarbamoyl)-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000038
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(2-hydroxyethyl)carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000032
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(3-hydroxypropyl)carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000001
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(3-phenylpropyl)carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000014
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(cyclopentyloxy)carbonyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000002
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(propan-2-yloxy)carbonyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000044
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[(tetrahydro-2H-pyran-4-yloxy)carbonyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000013
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(1H-imidazol-4-yl)ethyl]carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000014
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyrazin-2-yl)ethyl]carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000014
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-2-yl)ethyl]carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000014
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-3-yl)ethyl]carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000017
1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-N-[[2-(pyridin-4-yl)ethyl]carbamoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.00000086
2-phenylethanamine
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0358
flavimycin A
Staphylococcus aureus
-
pH and temperature not specified in the publication
0.1001
flavimycin B
Staphylococcus aureus
-
pH and temperature not specified in the publication
0.0000017
N-(benzylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000009
N-(cyclobutylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000005
N-(cyclobutylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.00000093
N-(cyclohexylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000037
N-(cyclohexylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.00000052
N-(cyclopentylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000025
N-(cyclopentylcarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000034
N-(tert-butoxycarbonyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000012
N-(tert-butylcarbamoyl)-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.000012
N-acetyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000052
N-benzoyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000022
N-carbamoyl-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0022
N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
Staphylococcus aureus
-
i.e. SB 543668, IC50: 0.0022 mM
0.00025
N-formyl-N-hydroxy-3-phenylpropylamine
Staphylococcus aureus
-
i.e. SB 485345, IC50: 0.00025 mM
0.00109
N-hydroxy-N-[3-(6-methylpyridine-2-yl)propyl]formamide
Staphylococcus aureus
-
i.e. SB 505684, IC50: 0.00109 mM
0.0000023
N-[(2-aminoethyl)carbamoyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000033
N-[(3-amino-3-oxopropyl)carbamoyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000024
N-[(cyclobutyloxy)carbonyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000015
N-[(cyclohexyloxy)carbonyl]-1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolinamide
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000059
piperidin-4-yl [1-[(2R)-3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl]-L-prolyl]carbamate
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
0.0000016
propan-2-amine
Staphylococcus aureus
-
in 50 mM potassium phosphate (pH 7.6), at 25°C
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(2-methylphenyl)-L-prolinamide
0.0008
5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
0.0023
5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
Staphylococcus aureus
pH and temperature not specified in the publication
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(2-methylphenyl)-L-prolinamide
Staphylococcus aureus
-
6.25 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(3-methylphenyl)-L-prolinamide
Staphylococcus aureus
-
0.195 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methoxyphenyl)-L-prolinamide
Staphylococcus aureus
-
0.78 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methylphenyl)-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-morpholin-4-ylphenyl)-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-piperidin-1-ylphenyl)-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-pyrrolidin-1-ylphenyl)-L-prolinamide
Staphylococcus aureus
-
0.78 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(1H-pyrrol-1-yl)phenyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-methylpiperazin-1-yl)phenyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-oxidomorpholin-4-yl)phenyl]-L-prolinamide
Staphylococcus aureus
-
larger than 6.25 microg/ml
additional information
N-(3,4-difluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(3-chloro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(3-chloro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.195 microg/ml
additional information
N-(3-chloro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.195 microg/ml
additional information
N-(3-fluoro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(3-fluoro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(3-fluoro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(4-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-(4-fluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-[3-chloro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
3.13 microg/ml
additional information
N-[3-fluoro-4-(1-oxidopiperidin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
3.13 microg/ml
additional information
N-[3-fluoro-4-(1H-pyrrol-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.39 microg/ml
additional information
N-[3-fluoro-4-(4-methyl-1,4-diazepan-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
0.78 microg/ml
additional information
N-[3-fluoro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
3.13 microg/ml
additional information
N-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
1.56 microg/ml
additional information
N-[4-(4-ethylpiperazin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
Staphylococcus aureus
-
3.13 microg/ml
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
metabolism
the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview
physiological function
physiological function
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'
physiological function
enzyme PDF plays an important role in bacterial protein maturation, growth, and survival by degradation of the N-formyl group for the polypeptide
physiological function
peptide deformylase (PDF) catalyzes the removal of a formyl group from newly synthesized proteins
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
-
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
physiological function
-
peptide deformylase catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
crystal structure of Staphylococcus aureus peptide deformylase, SaPDF, in complex with its inhibitor actinonin at 1.9 A resolution
-
Ni-peptide deformylase from Pseudomonas aeruguinosa was co-crystallized with inhibitor
-
purified recombinant His6-tagged enzyme in complex with four hydroxamate inhibitors, hanging drop vapour-diffusion method, mixing of 30 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 120 mM NaCl, with reservoir solution consisting of 23% w/v PEG 4000, 50 mM Tris-HCl pH 8.5, 15% v/v glycerol, 100 mM MgCl2, 20mM CaCl2, X-ray diffraction structure determination and analysis at resolutions of 1.90-2.30 A
-
sitting-drop vapour-diffusion method, structure determination to 1.9 A resolution
-
sitting-drop vapour-diffusion method. Preparation of diffraction-quality Se-Met crystals of peptide deformylase that belong to space group C222(1) with unit cell parameters of a = 94.1 A, b = 121.9 A, c = 47.6 A, 1.9 resolution. Preparation of crystals with the inhibitors thiorphan, actinonin and PONU-172550. The thiorphan and actinonin co-crystals belong to space group C222(1). Repeated attempts to generate a complex structure of peptide deformylase with PNU-172550 from the orthorhombic space group are unsuccessful. Crystallization screening identifies an alternate C2 crystal form with unit cell dimensions of a = 93.4, b = 42.5, c = 104.1 A, beta = 93°
-
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
-
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PDF has high activity in Tris buffer, but low activity in HEPES and NaH2PO4 buffers
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
instable towards oxidation due to the oxidation of the metal ligating cysteine residue
666015
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, stable without catalase for more than 1 year when stored in 50% glycerol
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified by two chromatographic steps involving affinity and gel filtration columns
-
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain C41 (DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
for expession in Escherichia coli C41(DE3) cells with a C-terminal eight-residue, LEHHHHHH, tag
-
recombinant overexpression of C-terminally His6-tagged enzyme in Escherichia coli strain C41 (DE3)
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
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), a metalloprotease, is an important antibacterial drug target
drug development
the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview
medicine
-
peptide deformylase has been considered an attractive target for antibacterial chemotherapy
medicine
-
peptide deformylase represents a target for the discovery of broad spectrum antibacterial drugs
medicine
-
target for antibacterial agents against Staphylococcus aureus
medicine
-
the gene encoding peptide deformylase is present in all sequenced pathogenic bacterial genomes, therefore peptide deformylase is an attractive target for antibacterial chemotherapy
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.
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
Harris, M.S.; Bock, J.H.; Choi, G.; Cialdella, J.S.; Curry, K.A.; Deibel, M.R., Jr.; Jacobsen, E.J.; Marshall, V.P.; Murray, R.W., Jr.; Vosters, A.F.; Wolfe, C.L.; Yem, A.W.; Baldwin, E.T.
Co-crystallization of Staphylococcus aureus peptide deformylase (PDF) with potent inhibitors
Acta Crystallogr. Sect. D
58
2153-2156
2002
Staphylococcus aureus
Baldwin, E.T.; Harris, M.S.; Yem, A.W.; Wolfe, C.L.; Vosters, A.F.; Curry, K.A.; Murray, R.W.; Bock, J.H.; Marshall, V.P.; Cialdella, J.I.; Merchant, M.H.; Choi, G.; Deibel, M.R., Jr.
Crystal structure of type II peptide deformylase from Staphylococcus aureus
J. Biol. Chem.
277
31163-31171
2002
Staphylococcus aureus
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)
Molteni, V.; He, X.; Nabakka, J.; Yang, K.; Kreusch, A.; Gordon, P.; Bursulaya, B.; Warner, I.; Shin, T.; Biorac, T.; Ryder, N.S.; Goldberg, R.; Doughty, J.; He, Y.
Identification of novel potent bicyclic peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
14
1477-1481
2004
Staphylococcus aureus
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)
Yoon, H.; Kim, H.L.; Lee, S.; Kim, H.; Kim, H.; Lee, J.Y.; Mikami, B.; Suh, S.W.
Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent
Proteins
57
639-642
2004
Staphylococcus aureus
Wang, Z.; Zhou, W.
Synthesis and in vitro antibacterial activity of (2S)-N-(substitutedphenyl)-1-[(2R)-2-[(formylhydroxyamino)methyl]-1-oxohexyl]-2-pyrrolidinecarboxamides as potential peptide deformylase inhibitors
Chem. Biol. Drug Des.
73
142-146
2009
Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus enteridis, Staphylococcus non-hemolyticus
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
Shi, W.; Ma, H.; Duan, Y.; Aubart, K.; Fang, Y.; Zonis, R.; Yang, L.; Hu, W.
Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
21
1060-1063
2011
Staphylococcus aureus, Staphylococcus aureus ATCC 25923, Staphylococcus aureus ATCC 29213, Staphylococcus aureus ATCC 43300, Staphylococcus epidermidis, Staphylococcus epidermidis ATCC 12228
Axten, J.M.; Medina, J.R.; Blackledge, C.W.; Duquenne, C.; Grant, S.W.; Bobko, M.A.; Peng, T.; Miller, W.H.; Pinckney, T.; Gallagher, T.F.; Kulkarni, S.; Lewandowski, T.; Van Aller, G.S.; Zonis, R.; Ward, P.; Campobasso, N.
Acylprolinamides: A new class of peptide deformylase inhibitors with in vivo antibacterial activity
Bioorg. Med. Chem. Lett.
22
4028-4032
2012
Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus
Ananthula, R.S.; Ravikumar, M.; Mahmood, S.K.; Kumar, M.N.
Insights from ligand and structure based methods in virtual screening of selective Ni-peptide deformylase inhibitors
J. Mol. Model.
18
693-708
2012
Staphylococcus aureus (P68826)
Che, X.; Hu, J.; Wang, L.; Zhu, Z.; Xu, Q.; Lv, J.; Fu, Z.; Sun, Y.; Sun, J.; Lin, G.; Lu, R.; Yao, Z.
Expression, purification, and activity assay of peptide deformylase from Escherichia coli and Staphylococcus aureus
Mol. Cell. Biochem.
357
47-54
2011
Staphylococcus aureus, Staphylococcus aureus Mu50
Lee, S.J.; Lee, S.J.; Lee, S.K.; Yoon, H.J.; Lee, H.H.; Kim, K.K.; Lee, B.J.; Lee, B.I.; Suh, S.W.
Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
Acta Crystallogr. Sect. D
68
784-793
2012
Staphylococcus aureus, Staphylococcus aureus ATCC 6538p
O'Dwyer, K.; Hackel, M.; Hightower, S.; Hoban, D.; Bouchillon, S.; Qin, D.; Aubart, K.; Zalacain, M.; Butler, D.
Comparative analysis of the antibacterial activity of a novel peptide deformylase inhibitor, GSK1322322
Antimicrob. Agents Chemother.
57
2333-2342
2013
Moraxella catarrhalis, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyogenes, Streptomyces pneumoniae
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
Kwon, Y.J.; Sohn, M.J.; Kim, C.J.; Koshino, H.; Kim, W.G.
Flavimycins A and B, dimeric 1,3-dihydroisobenzofurans with peptide deformylase inhibitory activity from Aspergillus flavipes
J. Nat. Prod.
75
271-274
2012
Staphylococcus aureus
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)
Liang, L.; Zhou, Q.; Hao, Z.; Wang, F.; Zhu, Y.; Lin, Q.; Gao, J.
The discovery of antibacterial natural compound based on peptide deformylase
Comb. Chem. High Throughput Screen.
21
292-297
2018
Staphylococcus aureus (P68826), Staphylococcus aureus
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)
Liang, J.H.; Huo, X.K.; Cheng, Z.B.; Sun, C.P.; Zhao, J.C.; Kang, X.H.; Zhang, T.Y.; Chen, Z.J.; Yang, T.M.; Wu, Y.Y.; Deng, X.P.; Zhang, Y.X.
An indole diterpenoid isolated from the fungus Drechmeria sp. and its antimicrobial activity
Nat. Prod. Res.
33
2770-2776
2019
Staphylococcus aureus (P68826), Staphylococcus aureus, Staphylococcus aureus CGMCC 1.8721 (P68826)
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