Structure of PDB 2w4i Chain E Binding Site BS02

Receptor Information
>2w4i Chain E (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 E Residue 1256 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure 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]
PDB2w4i Potent and selective inhibitors of Helicobacter pylori glutamate racemase (MurI): pyridodiazepine amines.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		T41 S143 V146 P147 E150 E151
Binding residue
(residue number reindexed from 1)		T41 S143 V146 P147 E150 E151
Annotation score1
Binding affinityMOAD: ic50=0.5uM
BindingDB: IC50=500nM
Enzymatic activity
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)

[Back to BioLiP]