Structure of PDB 2jfz Chain B Binding Site BS01

Receptor Information
>2jfz Chain B (length=248) 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
LPTPPLLIHSGDAIVEYLQQKYALPKVEFHASGDVIWLERQAKEWLKL
Ligand information
Ligand ID003
InChIInChI=1S/C26H25N5O2/c1-17(2)15-30-24-22(25(32)29(3)26(30)33)23(19-11-13-27-14-12-19)31(28-24)16-20-9-6-8-18-7-4-5-10-21(18)20/h4-14,17H,15-16H2,1-3H3
InChIKeyNNZDBCPMOOEFTE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CN1c2c(c(n(n2)Cc3cccc4c3cccc4)c5ccncc5)C(=O)N(C1=O)C
ACDLabs 10.04O=C3c2c(c1ccncc1)n(nc2N(C(=O)N3C)CC(C)C)Cc5c4ccccc4ccc5
CACTVS 3.341CC(C)CN1C(=O)N(C)C(=O)c2c1nn(Cc3cccc4ccccc34)c2c5ccncc5
FormulaC26 H25 N5 O2
Name5-METHYL-7-(2-METHYLPROPYL)-2-(NAPHTHALEN-1-YLMETHYL)-3-PYRIDIN-4-YL-2H-PYRAZOLO[3,4-D]PYRIMIDINE-4,6(5H,7H)-DIONE
ChEMBLCHEMBL401874
DrugBank
ZINCZINC000029045993
PDB chain2jfz Chain B Residue 1256 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2jfz Exploitation of Structural and Regulatory Diversity in Glutamate Racemases
Resolution1.86 Å
Binding residue
(original residue number in PDB)		V10 G11 K17 I149 S152 H183 L186 Q248 W252
Binding residue
(residue number reindexed from 1)		V10 G11 K17 I149 S152 H183 L186 Q241 W245
Annotation score1
Binding affinityMOAD: Ki=5.8uM
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:2jfz, PDBe:2jfz, PDBj:2jfz
PDBsum2jfz
PubMed17568739
UniProtQ9ZLT0|MURI_HELPJ Glutamate racemase (Gene Name=murI)

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