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Literature summary for 3.5.1.88 extracted from
- Peptide deformylase a new target in antibacterial, antimalarial and anticancer drug discovery (2015), Curr. Med. Chem., 22, 214-236 .
Application
| Application | Comment | Organism |
|---|---|---|
| drug development | the enzyme HsPDF is a cancer therapeutic target | Homo sapiens |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Escherichia coli |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Mycobacterium tuberculosis |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Staphylococcus aureus |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Bacillus subtilis |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Helicobacter pylori |
| drug development | the enzyme is a drug target for antibacterial agents. Classification of PDF inhibitors, overview | Haemophilus influenzae |
| drug development | the enzyme is a drug target in malaria treatment | Plasmodium falciparum |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| cloning of the nuclear encoded gene of the apicoplast-localized PfPDF, functional recombinant expression in Escherichia coli | Plasmodium falciparum |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| PBD ID 3G5K | Homo sapiens |
| PDB ID 1BS8 | Plasmodium falciparum |
| PDB ID 2AI9 | Staphylococcus aureus |
| PDB IDs 1DFF and 1BS7 | Escherichia coli |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| (2R)-2-(2-cyclopentylethyl)-N4-hydroxy-N1-[(2S)-1-[(2R)-2-hydroxypyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]butanediamide | - |
Plasmodium falciparum |  |
| (2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide | an actinonin derivative | Escherichia coli | |
| (2R)-N-[6-carbamimidamido-1-(naphthalen-2-yl)-2-oxohexan-3-yl]-2-(sulfanylmethyl)hexanamide | - |
Escherichia coli | |
| (2R)-N4-hydroxy-N1-[(2S)-3-methyl-1-oxo-1-(piperidin-1-yl)butan-2-yl]-2-pentylbutanediamide | - |
Homo sapiens | |
| (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 | |
| (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 | |
| (2S)-N1-(2-cyclopentylethyl)-N2-(4,5-dimethyl-1,3-thiazol-2-yl)-N1-[2-(hydroxyamino)-2-oxoethyl]pyrrolidine-1,2-dicarboxamide | - |
Escherichia coli | |
| (2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide | - |
Escherichia coli | |
| (2Z)-2-(3-butyl-1,3-benzothiazol-2(3H)-ylidene)-N-hydroxyacetamide | active against Staphylococcus aureus strains | Staphylococcus aureus | |
| (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 | |
| 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 | |
| 1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide | - |
Escherichia coli | |
| 1-[(2R)-2-[(2S)-1-(hydroxyamino)-1-oxopropan-2-yl]hexanoyl]-N-propyl-L-prolinamide | active against Staphylococcus aureus strains | Staphylococcus aureus | |
| 2,3-dichloro-N-[2-[formyl(hydroxy)amino]ethyl]benzamide | active against Haemophilus influenzae strains | Haemophilus influenzae | |
| 2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | broadly active versus Escherichia coli and Bacillus subtilis strains | Bacillus subtilis | |
| 2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | broadly active versus Escherichia coli and Bacillus subtilis strains | Escherichia coli | |
| 2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide | - |
Escherichia coli | |
| 2-(2,2-dioxo-1,4-dihydro-2lambda6,1,3-benzothiadiazin-3(2H)-yl)-N-hydroxyacetamide | - |
Staphylococcus aureus | |
| 2-(4-formyl-3,5-diiodophenyl)-N-hydroxyacetamide | - |
Escherichia coli | |
| 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | broadly active versus Escherichia coli and Bacillus subtilis strains | Bacillus subtilis | |
| 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | broadly active versus Escherichia coli and Bacillus subtilis strains | Escherichia coli | |
| 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | - |
Homo sapiens | |
| 2-hydroxy-4-phenoxybutanal | active against Haemophilus influenzae strains | Haemophilus influenzae | |
| 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 | |
| 2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide | potently active versus Bacillus subtilis strains | Bacillus subtilis | |
| 2-[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]-N-hydroxyacetamide | - |
Escherichia coli | |
| 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 | |
| 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-methoxy-7-methyl-1,3-dihydro-2-benzofuran-4,5,6-triol | has antibacterial activity on Staphylococcus aureus strains | Staphylococcus aureus | |
| 4'-(2-ethyl-6,8-dimethylimidazo[1,2-b]pyridazin-3-yl)[1,1'-biphenyl]-2-carboxylic acid | - |
Escherichia coli | |
| 4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol | has antibacterial activity on Staphylococcus aureus strains | Staphylococcus aureus | |
| 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 | |
| 5-([[(1-benzothiophen-2-yl)methyl]sulfanyl]methyl)-N-hydroxy-1,2-oxazole-3-carboxamide | poor antibacterial activity | Escherichia coli | |
| 5-amino-1,3,4-thiadiazole-2-thiol | a slow-binding inhibitor of Escherichia coli Ni-PDF inhibitor upon aging | Escherichia coli | |
| 5-chloro-2-propyl-3-[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]-3H-imidazo[4,5-b]pyridine | - |
Escherichia coli | |
| 5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide | poor antibacterial activity | Staphylococcus aureus | |
| 6,7-dibromo-3-(3,4-dimethoxy-5-methylbenzoyl)-1-benzofuran-4(5H)-one | - |
Homo sapiens | |
| 6,7-dichloro-3-(3,4-dimethoxybenzoyl)-1-benzofuran-4,5-dione | - |
Homo sapiens | |
| actinonin | - |
Bacillus subtilis | |
| actinonin | - |
Escherichia coli | |
| actinonin | - |
Haemophilus influenzae | |
| actinonin | - |
Helicobacter pylori | |
| actinonin | - |
Homo sapiens | |
| actinonin | - |
Mycobacterium tuberculosis | |
| actinonin | - |
Plasmodium falciparum | |
| actinonin | - |
Staphylococcus aureus | |
| BB-83698 | - |
Bacillus subtilis | |
| BB-83698 | - |
Escherichia coli | |
| BB-83698 | - |
Haemophilus influenzae | |
| BB-83698 | - |
Helicobacter pylori | |
| BB-83698 | - |
Mycobacterium tuberculosis | |
| BB-83698 | - |
Staphylococcus aureus | |
| calpeptin | - |
Bacillus subtilis | |
| calpeptin | - |
Escherichia coli | |
| ethyl 1-(N-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl]-L-valyl)piperidine-3-carboxylate | - |
Homo sapiens | |
| fumimycin | - |
Bacillus subtilis | |
| fumimycin | isolated from the fermentation broth of Aspergillus fumisynnematus strain F746 | Staphylococcus aureus | |
| GSK-1322322 | - |
Bacillus subtilis | |
| GSK-1322322 | - |
Escherichia coli | |
| GSK-1322322 | - |
Haemophilus influenzae | |
| GSK-1322322 | - |
Helicobacter pylori | |
| GSK-1322322 | - |
Mycobacterium tuberculosis | |
| GSK-1322322 | - |
Staphylococcus aureus | |
| hematoxylin | - |
Homo sapiens | |
| LBM-415 | - |
Bacillus subtilis | |
| LBM-415 | - |
Escherichia coli | |
| LBM-415 | - |
Haemophilus influenzae | |
| LBM-415 | - |
Helicobacter pylori | |
| LBM-415 | - |
Mycobacterium tuberculosis | |
| LBM-415 | - |
Staphylococcus aureus | |
| macrolactin N | - |
Bacillus subtilis | |
| macrolactin N | isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains | Escherichia coli | |
| macrolactin N | isolated from Bacillus subtilis culture medium, has antibacterial activity on Staphylococcus aureus and Escherichia coli strains | Staphylococcus aureus | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Bacillus subtilis | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview. Poor inhibition by 23 and 24 | Escherichia coli | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Haemophilus influenzae | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Helicobacter pylori | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Homo sapiens | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Mycobacterium tuberculosis | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Plasmodium falciparum | |
| additional information | different classes of PDF inhibitors, structures, and molecular modeling studies, overview | Staphylococcus aureus | |
| N-(3-chloro-2,4-dimethylphenyl)-1-[(2S)-2-[(1S)-2-(hydroxyamino)-1-(hydroxysulfanyl)-2-oxoethyl]hexanoyl]-L-prolinamide | - |
Plasmodium falciparum | |
| N-(4-nitrophenyl)-N2-[2-(sulfanylmethyl)hexanoyl]lysinamide | - |
Plasmodium falciparum | |
| 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 | |
| N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide | - |
Escherichia coli | |
| N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide | - |
Staphylococcus aureus | |
| N-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,3lambda4,2,4-benzodithiadiazin-2-yl)acetamide | - |
Escherichia coli | |
| N-hydroxy-N2-[(1-hydroxycyclopentyl)(phenyl)acetyl]valinamide | - |
Plasmodium falciparum | |
| N-[(2R)-2-(cyclopentylmethyl)-3-[2-(furan-2-carbonyl)-1,2-diazinan-1-yl]-3-oxopropyl]-N-hydroxyformamide | - |
Escherichia coli | |
| N-[(2S)-2-[(2R)-2-(1,3-benzoxazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide | active against Mycobacterium tuberculosis strains | Mycobacterium tuberculosis | |
| N-[(2S)-2-[(2R)-2-(1H-benzimidazol-2-yl)pyrrolidine-1-carbonyl]hexyl]-N-hydroxyformamide | active against Mycobacterium tuberculosis strains | Mycobacterium tuberculosis | |
| 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 | |
| N-[(4-formyl-3,5-diiodophenyl)methyl]-N-hydroxyformamide | - |
Escherichia coli | |
| 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 | |
| N-[4'-(2-cyclopropyl-5,7-dimethylpyrazolo[1,5-a]pyrimidin-3-yl)[1,1'-biphenyl]-2-sulfonyl]benzamide | - |
Escherichia coli | |
| N-[[(3S,6R)-3-tert-butyl-2,5-dioxo-1,4-diazacyclopentadecan-6-yl]methyl]-N-hydroxyacetamide | - |
Escherichia coli | |
| N2-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-N-phenyl-L-lysinamide | - |
Plasmodium falciparum | |
| N2-(benzenesulfinyl)-N2-butyl-N-hydroxyglycinamide | - |
Escherichia coli | |
| N2-(benzenesulfonyl)-N2-butyl-N-hydroxyglycinamide | - |
Escherichia coli | |
| N2-[(2R)-2-[[hydroxy(oxo)-lambda5-phosphanyl]oxy]hexanoyl]-N-(4-nitrophenyl)-D-leucinamide | - |
Escherichia coli | |
| N2-[(benzyloxy)carbonyl]-N-[(2S)-1-oxohexan-2-yl]-L-leucinamide | - |
Bacillus subtilis | |
| puppurogallin | - |
Homo sapiens | |
| theaflavin | - |
Homo sapiens | |
| [4-(4-hydroxyphenoxy)-3,5-diiodophenyl]acetic acid | - |
Escherichia coli | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| apicoplast | nuclear encoded gene of the apicoplast-localized PfPDF | Plasmodium falciparum | 20011 | - |
| mitochondrion | - |
Homo sapiens | 5739 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Co2+ | activates and stabilizes | Escherichia coli | |
| Co2+ | activates and stabilizes | Mycobacterium tuberculosis | |
| Co2+ | activates and stabilizes | Staphylococcus aureus | |
| Co2+ | activates and stabilizes | Bacillus subtilis | |
| Co2+ | activates and stabilizes | Helicobacter pylori | |
| Co2+ | activates and stabilizes | Haemophilus influenzae | |
| Co2+ | required, enzyme binding structure analysis | Homo sapiens | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| Ni2+ | activates and stabilizes | Escherichia coli | |
| Ni2+ | activates and stabilizes | Mycobacterium tuberculosis | |
| Ni2+ | activates and stabilizes | Staphylococcus aureus | |
| Ni2+ | activates and stabilizes | Bacillus subtilis | |
| Ni2+ | activates and stabilizes | Helicobacter pylori | |
| Ni2+ | activates and stabilizes | Haemophilus influenzae | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | P94462 | type II PDF | - |
| Bacillus subtilis 168 | P94462 | type II PDF | - |
| Escherichia coli | P0A6K3 | type I PDF | - |
| Haemophilus influenzae | P44786 | - |
- |
| Haemophilus influenzae ATCC 51907 | P44786 | - |
- |
| Haemophilus influenzae DSM 11121 | P44786 | - |
- |
| Haemophilus influenzae KW20 | P44786 | - |
- |
| Haemophilus influenzae RD | P44786 | - |
- |
| Helicobacter pylori | P56419 | type I PDF | - |
| Helicobacter pylori 26695 | P56419 | type I PDF | - |
| Helicobacter pylori ATCC 700392 | P56419 | type I PDF | - |
| Homo sapiens | Q9HBH1 | type I PDF | - |
| Mycobacterium tuberculosis | P9WIJ3 | type I PDF | - |
| Mycobacterium tuberculosis ATCC 25618 | P9WIJ3 | type I PDF | - |
| Mycobacterium tuberculosis H37Rv | P9WIJ3 | type I PDF | - |
| Plasmodium falciparum | Q8I372 | type I PDF | - |
| Plasmodium falciparum isolate 3D7 | Q8I372 | type I PDF | - |
| Staphylococcus aureus | P68826 | type II PDF | - |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| 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 |
| 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 |
| 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 |
| 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
| Synonyms | Comment | Organism |
|---|---|---|
| Def1 | - |
Staphylococcus aureus |
| Def1 | - |
Bacillus subtilis |
| HpPDF | - |
Helicobacter pylori |
| HsPDF | - |
Homo sapiens |
- |
Escherichia coli | |
- |
Homo sapiens | |
- |
Mycobacterium tuberculosis | |
- |
Staphylococcus aureus | |
- |
Plasmodium falciparum | |
- |
Bacillus subtilis | |
- |
Helicobacter pylori | |
- |
Haemophilus influenzae | |
| PfPDF | - |
Plasmodium falciparum |
| type I PDF | - |
Escherichia coli |
| type I PDF | - |
Homo sapiens |
| type I PDF | - |
Mycobacterium tuberculosis |
| type I PDF | - |
Plasmodium falciparum |
| type I PDF | - |
Helicobacter pylori |
| type I PDF | - |
Haemophilus influenzae |
| type II PDF | - |
Staphylococcus aureus |
| type II PDF | - |
Bacillus subtilis |
Ki Value [mM]
| Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 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 | |
| 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 | |
| 0.0027 | - |
hematoxylin | pH and temperature not specified in the publication | Homo sapiens | |
| 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 | |
| 0.0061 | - |
theaflavin | pH and temperature not specified in the publication | Homo sapiens | |
| 0.0061 | - |
6,7-dichloro-3-(3,4-dimethoxybenzoyl)-1-benzofuran-4,5-dione | pH and temperature not specified in the publication | Homo sapiens | |
| 0.0088 | - |
puppurogallin | pH and temperature not specified in the publication | Homo sapiens | |
| 0.36 | - |
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | pH and temperature not specified in the publication | Homo sapiens | |
IC50 Value
| IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
|---|---|---|---|---|---|
| 0.000005 | - |
pH and temperature not specified in the publication | Staphylococcus aureus | N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide | |
| 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 | |
| 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 | |
| 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 | |
| 0.000008 | - |
pH and temperature not specified in the publication | Escherichia coli | 2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 0.00013 | - |
pH and temperature not specified in the publication | Escherichia coli | 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide | |
| 0.00013 | - |
pH and temperature not specified in the publication | Plasmodium falciparum | N2-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-N-phenyl-L-lysinamide | |
| 0.00031 | - |
pH and temperature not specified in the publication | Escherichia coli | N-hydroxy-2-(2-oxo-1,4-dihydroquinazolin-3(2H)-yl)acetamide | |
| 0.0008 | - |
pH and temperature not specified in the publication | Staphylococcus aureus | 5-[[(4-chlorophenyl)sulfanyl]methyl]-N-hydroxy-1,2-oxazole-3-carboxamide | |
| 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 | |
| 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 | |
| 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 | |
| 0.0036 | - |
pH and temperature not specified in the publication | Staphylococcus aureus | 4-methyl-1,3-dihydro-2-benzofuran-1,5,6,7-tetrol | |
| 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) | |
| 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 | |
| 0.00402 | - |
pH and temperature not specified in the publication | Helicobacter pylori | 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate | |
| 0.0041 | - |
pH and temperature not specified in the publication | Staphylococcus aureus | fumimycin | |
| 0.0075 | - |
pH and temperature not specified in the publication | Staphylococcus aureus | macrolactin N | |
| 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 | |
| 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 | |
| 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 | |
| 0.026 | - |
pH and temperature not specified in the publication, versus Fe-PDF enzyme | Escherichia coli | calpeptin | |
| 0.0556 | - |
pH and temperature not specified in the publication, versus Fe-PDF enzyme | Bacillus subtilis | calpeptin | |
| 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 | |
| 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
| General Information | Comment | Organism |
|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| malfunction | a decrease in human cell growth results from PDF inhibitors actinonin and its analogues | Homo sapiens |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Escherichia coli |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Homo sapiens |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Mycobacterium tuberculosis |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Staphylococcus aureus |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Plasmodium falciparum |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Bacillus subtilis |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Helicobacter pylori |
| metabolism | the PDF catalyzed deformylase reaction is part of the methionine molecular cycle, overview | Haemophilus influenzae |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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