Structure of PDB 2ew6 Chain A Binding Site BS02

Receptor Information
>2ew6 Chain A (length=166) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQ
VGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPG
FYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDK
LSILKRKKFEKELKEL
Ligand information
Ligand IDY13
InChIInChI=1S/C17H17NO4/c19-14-5-1-12(2-6-14)9-10-18-17(22)8-4-13-3-7-15(20)16(21)11-13/h1-8,11,19-21H,9-10H2,(H,18,22)/b8-4+
InChIKeyVSHUQLRHTJOKTA-XBXARRHUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NCCc1ccc(O)cc1)\C=C\c2cc(O)c(O)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1CCNC(=O)\C=C\c2ccc(c(c2)O)O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCNC(=O)C=Cc2ccc(c(c2)O)O)O
CACTVS 3.341Oc1ccc(CCNC(=O)C=Cc2ccc(O)c(O)c2)cc1
CACTVS 3.341Oc1ccc(CCNC(=O)\C=C\c2ccc(O)c(O)c2)cc1
FormulaC17 H17 N O4
Name(2E)-3-(3,4-DIHYDROXYPHENYL)-N-[2-(4-HYDROXYPHENYL)ETHYL]ACRYLAMIDE
ChEMBLCHEMBL206646
DrugBankDB08754
ZINCZINC000013515185
PDB chain2ew6 Chain A Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ew6 Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G44 I45 G46 Y92 E94 G95 C96 L97 P100 Y103 L131 V134 A135 H138 E139
Binding residue
(residue number reindexed from 1)		G43 I44 G45 Y91 E93 G94 C95 L96 P99 Y102 L130 V133 A134 H137 E138
Annotation score1
Binding affinityMOAD: ic50=10.8uM
PDBbind-CN: -logKd/Ki=4.97,IC50=10.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) G46 Q51 C96 L97 H138 E139 H142
Catalytic site (residue number reindexed from 1) G45 Q50 C95 L96 H137 E138 H141
Enzyme Commision number 3.5.1.88: peptide deformylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0042586 peptide deformylase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0018206 peptidyl-methionine modification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ew6, PDBe:2ew6, PDBj:2ew6
PDBsum2ew6
PubMed16882991
UniProtQ672W7

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