Structure of PDB 2w4i Chain B Binding Site BS02

Receptor Information
>2w4i Chain B (length=254) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQF
GLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAI
KRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIE
ESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFA
LPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAK
EWLK
Ligand information
Ligand IDVGA
InChIInChI=1S/C22H19N3OS/c26-16-13-25(14-16)22-21(19-11-6-12-27-19)24-20(15-7-2-1-3-8-15)17-9-4-5-10-18(17)23-22/h1-12,16,21,26H,13-14H2/t21-/m1/s1
InChIKeyBKSGACYTXOQQNI-OAQYLSRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1ccc(cc1)C2=N[C@@H](C(=Nc3c2cccc3)N4CC(C4)O)c5cccs5
OpenEye OEToolkits 1.6.1c1ccc(cc1)C2=NC(C(=Nc3c2cccc3)N4CC(C4)O)c5cccs5
CACTVS 3.352O[C@H]1CN(C1)C2=Nc3ccccc3C(=N[C@@H]2c4sccc4)c5ccccc5
CACTVS 3.352O[CH]1CN(C1)C2=Nc3ccccc3C(=N[CH]2c4sccc4)c5ccccc5
ACDLabs 10.04N2=C(c4ccccc4N=C(N1CC(O)C1)C2c3sccc3)c5ccccc5
FormulaC22 H19 N3 O S
Name1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL
ChEMBL
DrugBankDB08698
ZINCZINC000053194178
PDB chain2w4i Chain B Residue 1256 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2w4i Potent and selective inhibitors of Helicobacter pylori glutamate racemase (MurI): pyridodiazepine amines.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		P38 T41 V146 P147 E150 E151
Binding residue
(residue number reindexed from 1)		P38 T41 V146 P147 E150 E151
Annotation score1
Binding affinityMOAD: ic50=0.5uM
PDBbind-CN: -logKd/Ki=6.30,IC50=0.5uM
BindingDB: IC50=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) D7 S8 C70 E150 C181 H183
Catalytic site (residue number reindexed from 1) D7 S8 C70 E150 C181 H183
Enzyme Commision number 5.1.1.3: glutamate racemase.
Gene Ontology
Molecular Function
GO:0008881 glutamate racemase activity
GO:0016853 isomerase activity
GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
GO:0036361 racemase activity, acting on amino acids and derivatives
GO:0042802 identical protein binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2w4i, PDBe:2w4i, PDBj:2w4i
PDBsum2w4i
PubMed19097892
UniProtQ9ZLT0|MURI_HELPJ Glutamate racemase (Gene Name=murI)

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