Structure of PDB 4jvb Chain B Binding Site BS01

Receptor Information
>4jvb 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]
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPK
KILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNS
TNTWQSLIEAAQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand ID1M0
InChIInChI=1S/C38H32N4O/c1-2-13-31(42-36-21-12-10-19-34(36)40-38(42)29-16-7-4-8-17-29)27-43-32-24-22-30(23-25-32)37-39-33-18-9-11-20-35(33)41(37)26-28-14-5-3-6-15-28/h2-12,14-25,31H,1,13,26-27H2/t31-/m1/s1
InChIKeyVETKHSOXOHNPCG-WJOKGBTCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C=CCC(COc1ccc(cc1)c2nc3ccccc3n2Cc4ccccc4)n5c6ccccc6nc5c7ccccc7
CACTVS 3.370C=CC[CH](COc1ccc(cc1)c2nc3ccccc3n2Cc4ccccc4)n5c6ccccc6nc5c7ccccc7
ACDLabs 12.01n2c1ccccc1n(c2c6ccc(OCC(n4c5ccccc5nc4c3ccccc3)C\C=C)cc6)Cc7ccccc7
CACTVS 3.370
OpenEye OEToolkits 1.7.6		C=CC[C@H](COc1ccc(cc1)c2nc3ccccc3n2Cc4ccccc4)n5c6ccccc6nc5c7ccccc7
FormulaC38 H32 N4 O
Name1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
ChEMBL
DrugBank
ZINCZINC000098207989
PDB chain4jvb Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jvb Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
Resolution1.75 Å
Binding residue
(original residue number in PDB)		M20 L22 W32 V49 I53 R61 Q78 V80 I109 A111 M117 I129 L147 Y149
Binding residue
(residue number reindexed from 1)		M19 L21 W31 V48 I52 R60 Q77 V79 I108 A110 M113 I125 L143 Y145
Annotation score1
Binding affinityMOAD: Kd=39nM
PDBbind-CN: -logKd/Ki=7.41,Kd=39nM
BindingDB: Kd=39nM
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:4jvb, PDBe:4jvb, PDBj:4jvb
PDBsum4jvb
PubMed23698361
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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