Literature summary extracted from

Sangshetti, J.; Khan, F.; Shinde, D.
Peptide deformylase a new target in antibacterial, antimalarial and anticancer drug discovery (2015), Curr. Med. Chem., 22, 214-236 .

Application

EC Number	Application	Comment	Organism
3.5.1.88	drug development	the enzyme HsPDF is a cancer therapeutic target	Homo sapiens
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Escherichia coli
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Mycobacterium tuberculosis
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Staphylococcus aureus
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Bacillus subtilis
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Helicobacter pylori
3.5.1.88	drug development	the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview	Haemophilus influenzae
3.5.1.88	drug development	the enzyme is a drug target in malaria treatment	Plasmodium falciparum

Cloned(Commentary)

EC Number	Cloned (Comment)	Organism
3.5.1.88	cloning of the nuclear encoded gene of the apicoplast-localized PfPDF, functional recombinant expression in Escherichia coli	Plasmodium falciparum

Crystallization (Commentary)

EC Number	Crystallization (Comment)	Organism
3.5.1.88	PBD ID 3G5K	Homo sapiens
3.5.1.88	PDB ID 1BS8	Plasmodium falciparum
3.5.1.88	PDB ID 2AI9	Staphylococcus aureus
3.5.1.88	PDB IDs 1DFF and 1BS7	Escherichia coli

Inhibitors

EC Number	Inhibitors	Comment	Organism
3.5.1.88	(2R)-2-(2-cyclopentylethyl)-N4-hydroxy-N1-[(2S)-1-[(2R)-2-hydroxypyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]butanediamide	-	Plasmodium falciparum
3.5.1.88	(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide	an actinonin derivative	Escherichia coli
3.5.1.88	(2R)-N-[6-carbamimidamido-1-(naphthalen-2-yl)-2-oxohexan-3-yl]-2-(sulfanylmethyl)hexanamide	-	Escherichia coli
3.5.1.88	(2R)-N4-hydroxy-N1-[(2S)-3-methyl-1-oxo-1-(piperidin-1-yl)butan-2-yl]-2-pentylbutanediamide	-	Homo sapiens
3.5.1.88	(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	Escherichia coli
3.5.1.88	(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	Staphylococcus aureus
3.5.1.88	(2S)-N1-(2-cyclopentylethyl)-N2-(4,5-dimethyl-1,3-thiazol-2-yl)-N1-[2-(hydroxyamino)-2-oxoethyl]pyrrolidine-1,2-dicarboxamide	-	Escherichia coli
3.5.1.88	(2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide	-	Escherichia coli
3.5.1.88	(2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide	active against Staphylococcus aureus strains	Staphylococcus aureus
3.5.1.88	(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	Staphylococcus aureus
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide	-	Escherichia coli
3.5.1.88	1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide	active against Staphylococcus aureus strains	Staphylococcus aureus
3.5.1.88	2,3-dichloro-N-[2-[formyl(hydroxy)amino]ethyl]benzamide	active against Haemophilus influenzae strains	Haemophilus influenzae
3.5.1.88	2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	broadly active versus Escherichia coli and Bacillus subtilis strains	Bacillus subtilis
3.5.1.88	2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	broadly active versus Escherichia coli and Bacillus subtilis strains	Escherichia coli
3.5.1.88	2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide	-	Escherichia coli
3.5.1.88	2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide	-	Staphylococcus aureus
3.5.1.88	2-(4-formyl-3,5-diiodophenyl)-N-hydroxyacetamide	-	Escherichia coli
3.5.1.88	2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	broadly active versus Escherichia coli and Bacillus subtilis strains	Bacillus subtilis
3.5.1.88	2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	broadly active versus Escherichia coli and Bacillus subtilis strains	Escherichia coli
3.5.1.88	2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	-	Homo sapiens
3.5.1.88	2-hydroxy-4-phenoxybutanal	active against Haemophilus influenzae strains	Haemophilus influenzae
3.5.1.88	2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate	CAPE, does not chelate HpPDF and does not disrupt the metal-dependent catalysis	Helicobacter pylori
3.5.1.88	2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide	potently active versus Bacillus subtilis strains	Bacillus subtilis
3.5.1.88	2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide	-	Escherichia coli
3.5.1.88	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	Escherichia coli
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	3-methoxy-7-methyl-1,3-dihydro-2-benzofuran-4,5,6-triol	has antibacterial activity on Staphylococcus aureus strains	Staphylococcus aureus
3.5.1.88	4'-(2-ethyl-6,8-dimethylimidazo[1,2-b]pyridazin-3-yl)[1,1'-biphenyl]-2-carboxylic acid	-	Escherichia coli
3.5.1.88	4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol	has antibacterial activity on Staphylococcus aureus strains	Staphylococcus aureus
3.5.1.88	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	Escherichia coli
3.5.1.88	5-([[(1-benzothiophen-2-yl)methyl]sulfanyl]methyl)-N-hydroxy-1,2-oxazole-3-carboxamide	poor antibacterial activity	Escherichia coli
3.5.1.88	5-amino-1,3,4-thiadiazole-2-thiol	a slow-binding inhibitor of Escherichia coli Ni-PDF inhibitor upon aging	Escherichia coli
3.5.1.88	5-chloro-2-propyl-3-[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]-3H-imidazo[4,5-b]pyridine	-	Escherichia coli
3.5.1.88	5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide	poor antibacterial activity	Staphylococcus aureus
3.5.1.88	6,7-dibromo-3-(3,4-dimethoxy-5-methylbenzoyl)-1-benzofuran-4(5H)-one	-	Homo sapiens
3.5.1.88	6,7-dichloro-3-(3,4-dimethoxybenzoyl)-1-benzofuran-4,5-dione	-	Homo sapiens
3.5.1.88	actinonin	-	Bacillus subtilis
3.5.1.88	actinonin	-	Escherichia coli
3.5.1.88	actinonin	-	Haemophilus influenzae
3.5.1.88	actinonin	-	Helicobacter pylori
3.5.1.88	actinonin	-	Homo sapiens
3.5.1.88	actinonin	-	Mycobacterium tuberculosis
3.5.1.88	actinonin	-	Plasmodium falciparum
3.5.1.88	actinonin	-	Staphylococcus aureus
3.5.1.88	BB-83698	-	Bacillus subtilis
3.5.1.88	BB-83698	-	Escherichia coli
3.5.1.88	BB-83698	-	Haemophilus influenzae
3.5.1.88	BB-83698	-	Helicobacter pylori
3.5.1.88	BB-83698	-	Mycobacterium tuberculosis
3.5.1.88	BB-83698	-	Staphylococcus aureus
3.5.1.88	calpeptin	-	Bacillus subtilis
3.5.1.88	calpeptin	-	Escherichia coli
3.5.1.88	ethyl 1-(N-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl]-L-valyl)piperidine-3-carboxylate	-	Homo sapiens
3.5.1.88	fumimycin	-	Bacillus subtilis
3.5.1.88	fumimycin	isolated from the fermentation broth of Aspergillus fumisynnematus strain F746	Staphylococcus aureus
3.5.1.88	GSK-1322322	-	Bacillus subtilis
3.5.1.88	GSK-1322322	-	Escherichia coli
3.5.1.88	GSK-1322322	-	Haemophilus influenzae
3.5.1.88	GSK-1322322	-	Helicobacter pylori
3.5.1.88	GSK-1322322	-	Mycobacterium tuberculosis
3.5.1.88	GSK-1322322	-	Staphylococcus aureus
3.5.1.88	hematoxylin	-	Homo sapiens
3.5.1.88	LBM-415	-	Bacillus subtilis
3.5.1.88	LBM-415	-	Escherichia coli
3.5.1.88	LBM-415	-	Haemophilus influenzae
3.5.1.88	LBM-415	-	Helicobacter pylori
3.5.1.88	LBM-415	-	Mycobacterium tuberculosis
3.5.1.88	LBM-415	-	Staphylococcus aureus
3.5.1.88	macrolactin N	-	Bacillus subtilis
3.5.1.88	macrolactin N	isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains	Escherichia coli
3.5.1.88	macrolactin N	isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains	Staphylococcus aureus
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Bacillus subtilis
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview. Poor inhibition by 23 and 24	Escherichia coli
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Haemophilus influenzae
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Helicobacter pylori
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Homo sapiens
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Mycobacterium tuberculosis
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Plasmodium falciparum
3.5.1.88	additional information	different classes of PDF inhibitors, structures, and molecular modeling studies, overview	Staphylococcus aureus
3.5.1.88	N-(3-chloro-2,4-dimethylphenyl)-1-[(2S)-2-[(1S)-2-(hydroxyamino)-1-(hydroxysulfanyl)-2-oxoethyl]hexanoyl]-L-prolinamide	-	Plasmodium falciparum
3.5.1.88	N-(4-nitrophenyl)-N2-[2-(sulfanylmethyl)hexanoyl]lysinamide	-	Plasmodium falciparum
3.5.1.88	N-(cyclobutylcarbamoyl)-1-[(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl]-L-prolinamide	active against Staphylococcus aureus, Haemophilus influenzae, and Streptomyces pneumoniae strains	Staphylococcus aureus
3.5.1.88	N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide	-	Escherichia coli
3.5.1.88	N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide	-	Staphylococcus aureus
3.5.1.88	N-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,3lambda4,2,4-benzodithiadiazin-2-yl)acetamide	-	Escherichia coli
3.5.1.88	N-hydroxy-N2-[(1-hydroxycyclopentyl)(phenyl)acetyl]valinamide	-	Plasmodium falciparum
3.5.1.88	N-[(2R)-2-(cyclopentylmethyl)-3-[2-(furan-2-carbonyl)-1,2-diazinan-1-yl]-3-oxopropyl]-N-hydroxyformamide	-	Escherichia coli
3.5.1.88	N-[(2S)-2-[(2R)-2-(1,3-benzoxazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide	active against Mycobacterium tuberculosis strains	Mycobacterium tuberculosis
3.5.1.88	N-[(2S)-2-[(2R)-2-(1H-benzimidazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide	active against Mycobacterium tuberculosis strains	Mycobacterium tuberculosis
3.5.1.88	N-[(3,5-difluorophenyl)carbamoyl]-3-methyl-L-valyl-N2-cyclopentyl-N-hydroxyglycinamide	cytotoxic IC50 values for compound PMT497 are 0.0209 mM against MDA-MB-231 and 0.0212 mM against MDA-MB-468 cell lines	Homo sapiens
3.5.1.88	N-[(4-formyl-3,5-diiodophenyl)methyl]-N-hydroxyformamide	-	Escherichia coli
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	N-[4'-(2-cyclopropyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)[1,1'-biphenyl]-2-sulfonyl]benzamide	-	Escherichia coli
3.5.1.88	N-[[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]methyl]-N-hydroxyacetamide	-	Escherichia coli
3.5.1.88	N2-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-N-phenyl-L-lysinamide	-	Plasmodium falciparum
3.5.1.88	N2-(benzenesulfinyl)-N2-butyl-N-hydroxyglycinamide	-	Escherichia coli
3.5.1.88	N2-(benzenesulfonyl)-N2-butyl-N-hydroxyglycinamide	-	Escherichia coli
3.5.1.88	N2-[(2R)-2-[[hydroxy(oxo)-lambda5-phosphanyl]oxy]hexanoyl]-N-(4-nitrophenyl)-D-leucinamide	-	Escherichia coli
3.5.1.88	N2-[(benzyloxy)carbonyl]-N-[(2S)-1-oxohexan-2-yl]-L-leucinamide	-	Bacillus subtilis
3.5.1.88	puppurogallin	-	Homo sapiens
3.5.1.88	theaflavin	-	Homo sapiens
3.5.1.88	[4-(4-hydroxyphenoxy)-3,5-diiodophenyl]acetic acid	-	Escherichia coli

Localization

EC Number	Localization	Comment	Organism	GeneOntology No.	Textmining
3.5.1.88	apicoplast	nuclear encoded gene of the apicoplast-localized PfPDF	Plasmodium falciparum	20011	-
3.5.1.88	mitochondrion	-	Homo sapiens	5739	-

Metals/Ions

EC Number	Metals/Ions	Comment	Organism
3.5.1.88	Co2+	activates and stabilizes	Escherichia coli
3.5.1.88	Co2+	activates and stabilizes	Mycobacterium tuberculosis
3.5.1.88	Co2+	activates and stabilizes	Staphylococcus aureus
3.5.1.88	Co2+	activates and stabilizes	Bacillus subtilis
3.5.1.88	Co2+	activates and stabilizes	Helicobacter pylori
3.5.1.88	Co2+	activates and stabilizes	Haemophilus influenzae
3.5.1.88	Co2+	required, enzyme binding structure analysis	Homo sapiens
3.5.1.88	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	Escherichia coli
3.5.1.88	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	Mycobacterium tuberculosis
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	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	Bacillus subtilis
3.5.1.88	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	Helicobacter pylori
3.5.1.88	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	Haemophilus influenzae
3.5.1.88	Fe2+	the metal ion is positioned at the bottom of the pocket to enable the enzyme to carry out its catalytic function. The metal ion is tetrahedrally coordinated by three amino acid residues (Cys155, His196, and His200, respectively) and a water molecule	Plasmodium falciparum
3.5.1.88	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	Escherichia coli
3.5.1.88	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	Homo sapiens
3.5.1.88	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	Mycobacterium tuberculosis
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	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	Bacillus subtilis
3.5.1.88	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	Helicobacter pylori
3.5.1.88	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	Haemophilus influenzae
3.5.1.88	Ni2+	activates and stabilizes	Escherichia coli
3.5.1.88	Ni2+	activates and stabilizes	Mycobacterium tuberculosis
3.5.1.88	Ni2+	activates and stabilizes	Staphylococcus aureus
3.5.1.88	Ni2+	activates and stabilizes	Bacillus subtilis
3.5.1.88	Ni2+	activates and stabilizes	Helicobacter pylori
3.5.1.88	Ni2+	activates and stabilizes	Haemophilus influenzae

Organism

EC Number	Organism	UniProt	Comment	Textmining
3.5.1.88	Bacillus subtilis	P94462	type II PDF	-
3.5.1.88	Bacillus subtilis 168	P94462	type II PDF	-
3.5.1.88	Escherichia coli	P0A6K3	type I PDF	-
3.5.1.88	Haemophilus influenzae	P44786	-	-
3.5.1.88	Haemophilus influenzae ATCC 51907	P44786	-	-
3.5.1.88	Haemophilus influenzae DSM 11121	P44786	-	-
3.5.1.88	Haemophilus influenzae KW20	P44786	-	-
3.5.1.88	Haemophilus influenzae RD	P44786	-	-
3.5.1.88	Helicobacter pylori	P56419	type I PDF	-
3.5.1.88	Helicobacter pylori 26695	P56419	type I PDF	-
3.5.1.88	Helicobacter pylori ATCC 700392	P56419	type I PDF	-
3.5.1.88	Homo sapiens	Q9HBH1	type I PDF	-
3.5.1.88	Mycobacterium tuberculosis	P9WIJ3	type I PDF	-
3.5.1.88	Mycobacterium tuberculosis ATCC 25618	P9WIJ3	type I PDF	-
3.5.1.88	Mycobacterium tuberculosis H37Rv	P9WIJ3	type I PDF	-
3.5.1.88	Plasmodium falciparum	Q8I372	type I PDF	-
3.5.1.88	Plasmodium falciparum isolate 3D7	Q8I372	type I PDF	-
3.5.1.88	Staphylococcus aureus	P68826	type II PDF	-

Subunits

EC Number	Subunits	Comment	Organism
3.5.1.88	More	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	Escherichia coli
3.5.1.88	More	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	Staphylococcus aureus
3.5.1.88	More	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. Detailed analysis of the three-dimensional structure of human PDF with bound Co2+	Homo sapiens
3.5.1.88	More	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. The subunit structure of PfPDF consists of a mixed alpha/betatopology, with three anti-parallel beta-sheets, three major alpha-helices, and one small helix near the N-terminus	Plasmodium falciparum

Synonyms

EC Number	Synonyms	Comment	Organism
3.5.1.88	Def1	-	Staphylococcus aureus
3.5.1.88	Def1	-	Bacillus subtilis
3.5.1.88	HpPDF	-	Helicobacter pylori
3.5.1.88	HsPDF	-	Homo sapiens
3.5.1.88	PDF	-	Escherichia coli
3.5.1.88	PDF	-	Homo sapiens
3.5.1.88	PDF	-	Mycobacterium tuberculosis
3.5.1.88	PDF	-	Staphylococcus aureus
3.5.1.88	PDF	-	Plasmodium falciparum
3.5.1.88	PDF	-	Bacillus subtilis
3.5.1.88	PDF	-	Helicobacter pylori
3.5.1.88	PDF	-	Haemophilus influenzae
3.5.1.88	PfPDF	-	Plasmodium falciparum
3.5.1.88	type I PDF	-	Escherichia coli
3.5.1.88	type I PDF	-	Homo sapiens
3.5.1.88	type I PDF	-	Mycobacterium tuberculosis
3.5.1.88	type I PDF	-	Plasmodium falciparum
3.5.1.88	type I PDF	-	Helicobacter pylori
3.5.1.88	type I PDF	-	Haemophilus influenzae
3.5.1.88	type II PDF	-	Staphylococcus aureus
3.5.1.88	type II PDF	-	Bacillus subtilis

Ki Value [mM]

EC Number	Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism
3.5.1.88	0.000069	-	ethyl 1-(N-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl]-L-valyl)piperidine-3-carboxylate	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.000115	-	(2R)-N4-hydroxy-N1-[(2S)-3-methyl-1-oxo-1-(piperidin-1-yl)butan-2-yl]-2-pentylbutanediamide	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.0027	-	hematoxylin	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.0052	-	6,7-dibromo-3-(3,4-dimethoxy-5-methylbenzoyl)-1-benzofuran-4(5H)-one	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.0061	-	theaflavin	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.0061	-	6,7-dichloro-3-(3,4-dimethoxybenzoyl)-1-benzofuran-4,5-dione	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.0088	-	puppurogallin	pH and temperature not specified in the publication	Homo sapiens
3.5.1.88	0.36	-	2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide	pH and temperature not specified in the publication	Homo sapiens

IC50 Value

EC Number	IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor
3.5.1.88	0.000005	-	pH and temperature not specified in the publication	Staphylococcus aureus	N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
3.5.1.88	0.000005	-	pH and temperature not specified in the publication	Escherichia coli	N-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,3lambda4,2,4-benzodithiadiazin-2-yl)acetamide
3.5.1.88	0.000005	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	N-[(2R)-2-(cyclopentylmethyl)-3-[2-(furan-2-carbonyl)-1,2-diazinan-1-yl]-3-oxopropyl]-N-hydroxyformamide
3.5.1.88	0.000007	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide
3.5.1.88	0.000008	-	pH and temperature not specified in the publication	Escherichia coli	2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
3.5.1.88	0.00001	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Mycobacterium tuberculosis	N-[(2S)-2-[(2R)-2-(1H-benzimidazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide
3.5.1.88	0.000013	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Mycobacterium tuberculosis	N-[(2S)-2-[(2R)-2-(1,3-benzoxazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide
3.5.1.88	0.00002	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide
3.5.1.88	0.00012	-	pH and temperature not specified in the publication	Escherichia coli	2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide
3.5.1.88	0.00013	-	pH and temperature not specified in the publication	Escherichia coli	2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
3.5.1.88	0.00013	-	pH and temperature not specified in the publication	Plasmodium falciparum	N2-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-N-phenyl-L-lysinamide
3.5.1.88	0.00031	-	pH and temperature not specified in the publication	Escherichia coli	N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide
3.5.1.88	0.0008	-	pH and temperature not specified in the publication	Staphylococcus aureus	5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide
3.5.1.88	0.00104	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	(2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide
3.5.1.88	0.0025	-	pH and temperature not specified in the publication	Staphylococcus aureus	3-methoxy-7-methyl-1,3-dihydro-2-benzofuran-4,5,6-triol
3.5.1.88	0.0034	-	pH and temperature not specified in the publication	Escherichia coli	5-([[(1-benzothiophen-2-yl)methyl]sulfanyl]methyl)-N-hydroxy-1,2-oxazole-3-carboxamide
3.5.1.88	0.0036	-	pH and temperature not specified in the publication	Staphylococcus aureus	4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol
3.5.1.88	0.0037	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	5,5'-disulfanediyldi(1,3,4-thiadiazol-2-amine)
3.5.1.88	0.0039	-	pH and temperature not specified in the publication	Escherichia coli	4'-(2-ethyl-6,8-dimethylimidazo[1,2-b]pyridazin-3-yl)[1,1'-biphenyl]-2-carboxylic acid
3.5.1.88	0.00402	-	pH and temperature not specified in the publication	Helicobacter pylori	2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
3.5.1.88	0.0041	-	pH and temperature not specified in the publication	Staphylococcus aureus	fumimycin
3.5.1.88	0.0075	-	pH and temperature not specified in the publication	Staphylococcus aureus	macrolactin N
3.5.1.88	0.01	-	pH and temperature not specified in the publication	Escherichia coli	5-chloro-2-propyl-3-[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]-3H-imidazo[4,5-b]pyridine
3.5.1.88	0.015	-	pH and temperature not specified in the publication, versus Co-PDF enzyme	Bacillus subtilis	N2-[(benzyloxy)carbonyl]-N-[(2S)-1-oxohexan-2-yl]-L-leucinamide
3.5.1.88	0.0228	-	pH and temperature not specified in the publication	Escherichia coli	N-[4'-(2-cyclopropyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)[1,1'-biphenyl]-2-sulfonyl]benzamide
3.5.1.88	0.026	-	pH and temperature not specified in the publication, versus Fe-PDF enzyme	Escherichia coli	calpeptin
3.5.1.88	0.0556	-	pH and temperature not specified in the publication, versus Fe-PDF enzyme	Bacillus subtilis	calpeptin
3.5.1.88	0.076	-	pH and temperature not specified in the publication, versus Fe-PDF enzyme	Escherichia coli	N2-[(2R)-2-[[hydroxy(oxo)-lambda5-phosphanyl]oxy]hexanoyl]-N-(4-nitrophenyl)-D-leucinamide
3.5.1.88	0.129	-	pH and temperature not specified in the publication, versus Ni-PDF enzyme	Escherichia coli	5-amino-1,3,4-thiadiazole-2-thiol

General Information

EC Number	General Information	Comment	Organism
3.5.1.88	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	Homo sapiens
3.5.1.88	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	Mycobacterium tuberculosis
3.5.1.88	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	Plasmodium falciparum
3.5.1.88	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	Bacillus subtilis
3.5.1.88	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	Helicobacter pylori
3.5.1.88	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	Haemophilus influenzae
3.5.1.88	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	Escherichia coli
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	malfunction	a decrease in human cell growth results from PDF inhibitors actinonin and its analogues	Homo sapiens
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Escherichia coli
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Homo sapiens
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Mycobacterium tuberculosis
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Staphylococcus aureus
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Plasmodium falciparum
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Bacillus subtilis
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Helicobacter pylori
3.5.1.88	metabolism	the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview	Haemophilus influenzae
3.5.1.88	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'	Escherichia coli
3.5.1.88	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'	Homo sapiens
3.5.1.88	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'	Mycobacterium tuberculosis
3.5.1.88	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'	Staphylococcus aureus
3.5.1.88	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'	Plasmodium falciparum
3.5.1.88	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'	Bacillus subtilis
3.5.1.88	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'	Helicobacter pylori
3.5.1.88	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'	Haemophilus influenzae
3.5.1.88	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	Escherichia coli
3.5.1.88	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	Mycobacterium tuberculosis
3.5.1.88	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	Staphylococcus aureus
3.5.1.88	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	Bacillus subtilis
3.5.1.88	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	Helicobacter pylori
3.5.1.88	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	Haemophilus influenzae
3.5.1.88	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. In Plasmodium falciparum, formylation and deformylation process occurs in the apicoplast of the malaria parasite and plays important role in protein synthesis	Plasmodium falciparum
3.5.1.88	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. The mitochondrial localization of HsPDF, and N-formylation of human mitochondrial translation products for translation initiation point at the 13 proteins encoded by the mitochondrial genome as putative substrates of HsPDF	Homo sapiens