Structure of PDB 2xb9 Chain A Binding Site BS01

Receptor Information
>2xb9 Chain A (length=158) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFF
QTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIE
VHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKA
FQEAQKNN
Ligand information
Ligand IDXNW
InChIInChI=1S/C15H18O7/c1-22-9-4-2-8(3-5-9)6-10-12(17)13(18)11(16)7-15(10,21)14(19)20/h2-5,10-11,13,16,18,21H,6-7H2,1H3,(H,19,20)/t10-,11+,13-,15+/m0/s1
InChIKeyKDOXKRDIRCHNDT-YODMDTAWSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1ccc(C[CH]2C(=O)[CH](O)[CH](O)C[C]2(O)C(O)=O)cc1
OpenEye OEToolkits 1.6.1COc1ccc(cc1)CC2C(=O)C(C(CC2(C(=O)O)O)O)O
OpenEye OEToolkits 1.6.1COc1ccc(cc1)C[C@H]2C(=O)[C@H]([C@@H](C[C@@]2(C(=O)O)O)O)O
CACTVS 3.352COc1ccc(C[C@H]2C(=O)[C@@H](O)[C@H](O)C[C@]2(O)C(O)=O)cc1
ACDLabs 10.04O=C1C(O)C(O)CC(O)(C(=O)O)C1Cc2ccc(OC)cc2
FormulaC15 H18 O7
Name(1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID;
(2R)-2-METHOXYBENZYL-3-DEHYDROQUINIC ACID
ChEMBL
DrugBank
ZINCZINC000058638839
PDB chain2xb9 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xb9 Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		N10 Y22 N76 A79 H82 H102 L103 T104 R113
Binding residue
(residue number reindexed from 1)		N10 Y22 N76 A79 H82 H102 L103 T104 R113
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.77,Ki=0.17uM
Enzymatic activity
Catalytic site (original residue number in PDB) P9 N10 R17 Y22 N76 A79 E100 H102 R109
Catalytic site (residue number reindexed from 1) P9 N10 R17 Y22 N76 A79 E100 H102 R109
Enzyme Commision number 4.2.1.10: 3-dehydroquinate dehydratase.
Gene Ontology
Molecular Function
GO:0003855 3-dehydroquinate dehydratase activity
GO:0016829 lyase activity
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0009073 aromatic amino acid family biosynthetic process
GO:0009423 chorismate biosynthetic process
GO:0019631 quinate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2xb9, PDBe:2xb9, PDBj:2xb9
PDBsum2xb9
PubMed20815012
UniProtQ48255|AROQ_HELPY 3-dehydroquinate dehydratase (Gene Name=aroQ)

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