Structure of PDB 4jv6 Chain B Binding Site BS02

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 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jv6 Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
Resolution1.87 Å
Binding residue
(original residue number in PDB)		I53 L54 C56 W90 I109 A111 M117 L147 Y149
Binding residue
(residue number reindexed from 1)		I51 L52 C54 W88 I107 A109 M113 L143 Y145
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

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Molecular Function
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Biological Process
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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)

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