Structure of PDB 3cf9 Chain A Binding Site BS01

Receptor Information
>3cf9 Chain A (length=152) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNG
HFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKV
KFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAE
RE
Ligand information
Ligand IDAGI
InChIInChI=1S/C15H10O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-7,16-18H
InChIKeyKZNIFHPLKGYRTM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1ccc(cc1)C2=CC(=O)c3c(O)cc(O)cc3O2
OpenEye OEToolkits 1.5.0c1cc(ccc1C2=CC(=O)c3c(cc(cc3O2)O)O)O
ACDLabs 10.04O=C1c3c(OC(=C1)c2ccc(O)cc2)cc(O)cc3O
FormulaC15 H10 O5
Name5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one;
Apigenin
ChEMBLCHEMBL28
DrugBankDB07352
ZINCZINC000003871576
PDB chain3cf9 Chain A Residue 161 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cf9 Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay
Resolution2.6 Å
Binding residue
(original residue number in PDB)		F59 K62 F109 R110
Binding residue
(residue number reindexed from 1)		F52 K55 F102 R103
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.83,Ki=14.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) H58 I64 G67 V68 E72
Catalytic site (residue number reindexed from 1) H51 I57 G60 V61 E65
Enzyme Commision number 4.2.1.59: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0019171 (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3cf9, PDBe:3cf9, PDBj:3cf9
PDBsum3cf9
PubMed18780820
UniProtQ5G940

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