Structure of PDB 2xd9 Chain A Binding Site BS01

Receptor Information
>2xd9 Chain A (length=153) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFF
QTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIE
VHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKA
FQE
Ligand information
Ligand IDXD9
InChIInChI=1S/C12H14O5S/c1-2-3-6-4-7-10(18-6)9(14)8(13)5-12(7,17)11(15)16/h2-4,8-9,13-14,17H,5H2,1H3,(H,15,16)/b3-2+/t8-,9+,12-/m1/s1
InChIKeyXBFFFFBWIVSOII-PJMUFDJCSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C\C=C\c1sc2[C@@H](O)[C@H](O)C[C@](O)(C(O)=O)c2c1
OpenEye OEToolkits 1.6.1CC=Cc1cc2c(s1)C(C(CC2(C(=O)O)O)O)O
ACDLabs 10.04O=C(O)C2(O)c1c(sc(c1)/C=C/C)C(O)C(O)C2
CACTVS 3.352CC=Cc1sc2[CH](O)[CH](O)C[C](O)(C(O)=O)c2c1
OpenEye OEToolkits 1.6.1C\C=C\c1cc2c(s1)[C@H]([C@@H](C[C@@]2(C(=O)O)O)O)O
FormulaC12 H14 O5 S
Name(4R,6R,7S)-4,6,7-TRIHYDROXY-2-[(1E)-PROP-1-EN-1-YL]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID
ChEMBL
DrugBank
ZINCZINC000058638962
PDB chain2xd9 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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PDB2xd9 Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		N10 L14 Y22 N76 G78 A79 H82 H102 L103 T104 R113
Binding residue
(residue number reindexed from 1)		N10 L14 Y22 N76 G78 A79 H82 H102 L103 T104 R113
Annotation score1
Binding affinityMOAD: Ki=0.35uM
PDBbind-CN: -logKd/Ki=6.46,Ki=0.35uM
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:2xd9, PDBe:2xd9, PDBj:2xd9
PDBsum2xd9
PubMed21275050
UniProtQ48255|AROQ_HELPY 3-dehydroquinate dehydratase (Gene Name=aroQ)

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