Structure of PDB 4b1f Chain B Binding Site BS02

Receptor Information
>4b1f Chain B (length=255) 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
EWLKL
Ligand information
Ligand IDKRH
InChIInChI=1S/C25H26N6O2/c1-16(2)13-30-23-21(24(32)29(4)25(30)33)22(20-12-26-15-28(20)3)31(27-23)14-18-10-7-9-17-8-5-6-11-19(17)18/h5-12,15-16H,13-14H2,1-4H3
InChIKeyQJBUEINIMXZUED-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C3c2c(c1cncn1C)n(nc2N(C(=O)N3C)CC(C)C)Cc5c4ccccc4ccc5
CACTVS 3.385CC(C)CN1C(=O)N(C)C(=O)c2c1nn(Cc3cccc4ccccc34)c2c5cncn5C
OpenEye OEToolkits 1.9.2CC(C)CN1c2c(c(n(n2)Cc3cccc4c3cccc4)c5cncn5C)C(=O)N(C1=O)C
FormulaC25 H26 N6 O2
Name5-methyl-3-(1-methyl-1H-imidazol-5-yl)-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione
ChEMBLCHEMBL2088120
DrugBank
ZINCZINC000084703921
PDB chain4b1f Chain B Residue 1257 [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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PDB4b1f Design of Inhibitors of Helicobacter Pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles Onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		V10 G11 L186 Q248 W252
Binding residue
(residue number reindexed from 1)		V10 G11 L186 Q248 W252
Annotation score1
Binding affinityBindingDB: IC50=120nM
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:4b1f, PDBe:4b1f, PDBj:4b1f
PDBsum4b1f
PubMed22877632
UniProtQ9ZLT0|MURI_HELPJ Glutamate racemase (Gene Name=murI)

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