Structure of PDB 4b6s Chain C Binding Site BS01

Receptor Information
>4b6s Chain C (length=155) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFF
QTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIE
VHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKA
FQEAQ
Ligand information
Ligand ID2HN
InChIInChI=1S/C14H11F5O6/c15-6-3(7(16)9(18)10(19)8(6)17)1-4-11(21)12(22)5(20)2-14(4,25)13(23)24/h4-5,12,20,22,25H,1-2H2,(H,23,24)/t4-,5-,12+,14-/m1/s1
InChIKeyZNZHQTVBMHBUCF-GLOYCNQYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1C(C(O)(C(=O)O)CC(O)C1O)Cc2c(F)c(F)c(F)c(F)c2F
CACTVS 3.385O[C@@H]1C[C@@](O)([C@H](Cc2c(F)c(F)c(F)c(F)c2F)C(=O)[C@H]1O)C(O)=O
OpenEye OEToolkits 1.9.2C1[C@H]([C@@H](C(=O)[C@H]([C@]1(C(=O)O)O)Cc2c(c(c(c(c2F)F)F)F)F)O)O
OpenEye OEToolkits 1.9.2C1C(C(C(=O)C(C1(C(=O)O)O)Cc2c(c(c(c(c2F)F)F)F)F)O)O
CACTVS 3.385O[CH]1C[C](O)([CH](Cc2c(F)c(F)c(F)c(F)c2F)C(=O)[CH]1O)C(O)=O
FormulaC14 H11 F5 O6
Name(1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid;
(1R,2S,4S,5R)-2-(perfluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000095920626
PDB chain4b6s Chain A Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4b6s Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D89 L93
Binding residue
(residue number reindexed from 1)		D89 L93
Annotation score1
Binding affinityMOAD: Ki=970nM
PDBbind-CN: -logKd/Ki=6.01,Ki=970nM
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:4b6s, PDBe:4b6s, PDBj:4b6s
PDBsum4b6s
PubMed23198883
UniProtQ48255|AROQ_HELPY 3-dehydroquinate dehydratase (Gene Name=aroQ)

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