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Structure of PDB 3d04 Chain C Binding Site BS01

Receptor Information >3d04 Chain C (length=150) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGH FPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVK FRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER

Ligand information Ligand ID SAK InChI InChI=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 InChIKey DJOJDHGQRNZXQQ-AWEZNQCLSA-N SMILES Software SMILES OpenEye OEToolkits 1.5.0 COc1cc(c2c(c1)O[C@@H](CC2=O)c3ccc(cc3)O)O OpenEye OEToolkits 1.5.0 COc1cc(c2c(c1)OC(CC2=O)c3ccc(cc3)O)O CACTVS 3.341 COc1cc(O)c2C(=O)C[CH](Oc2c1)c3ccc(O)cc3 ACDLabs 10.04 O=C2c3c(OC(c1ccc(O)cc1)C2)cc(OC)cc3O CACTVS 3.341 COc1cc(O)c2C(=O)C[C@H](Oc2c1)c3ccc(O)cc3 Formula C16 H14 O5 Name (2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one; sakuranetin ChEMBL CHEMBL448297 DrugBank DB08517 ZINC ZINC000000338284 PDB chain 3d04 Chain C Residue 162 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 3d04 Three flavonoids targeting the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: crystal structure characterization with enzymatic inhibition assay Resolution 2.4 Å Binding residue (original residue number in PDB) H23 F83 K97 I98 V99 Binding residue (residue number reindexed from 1) H15 F75 K89 I90 V91 Annotation score 1 Binding affinity MOAD: Ki=0.9uM

Enzymatic activity Catalytic site (original residue number in PDB) H58 I64 G67 V68 E72 Catalytic site (residue number reindexed from 1) H50 I56 G59 V60 E64 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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