Structure of PDB 3d04 Chain A Binding Site BS01

Receptor Information
>3d04 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 IDSAK
InChIInChI=1S/C16H14O5/c1-20-11-6-12(18)16-13(19)8-14(21-15(16)7-11)9-2-4-10(17)5-3-9/h2-7,14,17-18H,8H2,1H3/t14-/m0/s1
InChIKeyDJOJDHGQRNZXQQ-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1cc(c2c(c1)O[C@@H](CC2=O)c3ccc(cc3)O)O
OpenEye OEToolkits 1.5.0COc1cc(c2c(c1)OC(CC2=O)c3ccc(cc3)O)O
CACTVS 3.341COc1cc(O)c2C(=O)C[CH](Oc2c1)c3ccc(O)cc3
ACDLabs 10.04O=C2c3c(OC(c1ccc(O)cc1)C2)cc(OC)cc3O
CACTVS 3.341COc1cc(O)c2C(=O)C[C@H](Oc2c1)c3ccc(O)cc3
FormulaC16 H14 O5
Name(2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one;
sakuranetin
ChEMBLCHEMBL448297
DrugBankDB08517
ZINCZINC000000338284
PDB chain3d04 Chain A Residue 163 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3d04 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)		F59 R110 I111 P112
Binding residue
(residue number reindexed from 1)		F52 R103 I104 P105
Annotation score1
Binding affinityMOAD: Ki=0.9uM
PDBbind-CN: -logKd/Ki=6.05,Ki=0.9uM
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:3d04, PDBe:3d04, PDBj:3d04
PDBsum3d04
PubMed18780820
UniProtQ5G940

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