Structure of PDB 3cf8 Chain B Binding Site BS01

Receptor Information
>3cf8 Chain B (length=149) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFP
NKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFR
IPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE
Ligand information
Ligand IDQUE
InChIInChI=1S/C15H10O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,16-19,21H
InChIKeyREFJWTPEDVJJIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1cc(O)c2C(=O)C(=C(Oc2c1)c3ccc(O)c(O)c3)O
OpenEye OEToolkits 1.5.0c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
ACDLabs 10.04O=C1c3c(OC(=C1O)c2ccc(O)c(O)c2)cc(O)cc3O
FormulaC15 H10 O7
Name3,5,7,3',4'-PENTAHYDROXYFLAVONE;
QUERCETIN
ChEMBLCHEMBL50
DrugBankDB04216
ZINCZINC000003869685
PDB chain3cf8 Chain A Residue 164 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cf8 Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I98 Y100
Binding residue
(residue number reindexed from 1)		I88 Y90
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.90,Ki=12.7uM
Enzymatic activity
Catalytic site (original residue number in PDB) H58 I64 G67 V68 E72
Catalytic site (residue number reindexed from 1) H48 I54 G57 V58 E62
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:3cf8, PDBe:3cf8, PDBj:3cf8
PDBsum3cf8
PubMed18780820
UniProtQ5G940

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