Structure of PDB 4jv6 Chain B Binding Site BS01

Receptor Information
>4jv6 Chain B (length=146) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKDERAREILRGFKLNWMNLRDATGKILWQGTEDLSVPGVEHEARVPKK
ILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNST
NTWQSLIEAASQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand ID18F
InChIInChI=1S/C20H16N2/c1-3-9-16(10-4-1)15-22-19-14-8-7-13-18(19)21-20(22)17-11-5-2-6-12-17/h1-14H,15H2
InChIKeyLCFXRSKBJWQHON-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)Cn2c3ccccc3nc2c4ccccc4
CACTVS 3.370C(n1c2ccccc2nc1c3ccccc3)c4ccccc4
ACDLabs 12.01n2c1ccccc1n(c2c3ccccc3)Cc4ccccc4
FormulaC20 H16 N2
Name1-benzyl-2-phenyl-1H-benzimidazole
ChEMBLCHEMBL1922082
DrugBank
ZINCZINC000000997179
PDB chain4jv6 Chain B Residue 201 [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]
PDB4jv6 Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
Resolution1.87 Å
Binding residue
(original residue number in PDB)		M20 W32 A47 R61 Q78 I129
Binding residue
(residue number reindexed from 1)		M19 W30 A45 R59 Q76 I125
Annotation score1
Binding affinityMOAD: Kd=217nM
PDBbind-CN: -logKd/Ki=6.66,Kd=217nM
BindingDB: Kd=2400nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005095 GTPase inhibitor activity
GO:0005515 protein binding
GO:0031267 small GTPase binding
Biological Process
GO:0007601 visual perception
GO:0050953 sensory perception of light stimulus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4jv6, PDBe:4jv6, PDBj:4jv6
PDBsum4jv6
PubMed23698361
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

[Back to BioLiP]