Structure of PDB 4jvf Chain B Binding Site BS01

Receptor Information
>4jvf Chain B (length=141) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKI
LKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTN
TWQSLIEAMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand ID17X
InChIInChI=1S/C40H42N6O2/c47-39(32-21-25-44(26-22-32)40-43-33-15-7-9-17-35(33)45(40)27-29-11-3-1-4-12-29)48-28-37(30-19-23-41-24-20-30)46-36-18-10-8-16-34(36)42-38(46)31-13-5-2-6-14-31/h1-18,30,32,37,41H,19-28H2/t37-/m1/s1
InChIKeyWDALFJYWTFDSRP-DIPNUNPCSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O=C(OC[C@H](C1CCNCC1)n2c3ccccc3nc2c4ccccc4)C5CCN(CC5)c6nc7ccccc7n6Cc8ccccc8
CACTVS 3.370O=C(OC[CH](C1CCNCC1)n2c3ccccc3nc2c4ccccc4)C5CCN(CC5)c6nc7ccccc7n6Cc8ccccc8
OpenEye OEToolkits 1.7.6c1ccc(cc1)Cn2c3ccccc3nc2N4CCC(CC4)C(=O)OCC(C5CCNCC5)n6c7ccccc7nc6c8ccccc8
OpenEye OEToolkits 1.7.6c1ccc(cc1)Cn2c3ccccc3nc2N4CCC(CC4)C(=O)OC[C@H](C5CCNCC5)n6c7ccccc7nc6c8ccccc8
ACDLabs 12.01O=C(OCC(n2c3ccccc3nc2c1ccccc1)C4CCNCC4)C8CCN(c5nc7c(n5Cc6ccccc6)cccc7)CC8
FormulaC40 H42 N6 O2
Name(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate
ChEMBLCHEMBL3286930
DrugBank
ZINCZINC000098207928
PDB chain4jvf 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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PDB4jvf Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M20 W32 L38 A47 I53 L54 C56 K57 R61 Q78 V80 L147 Y149
Binding residue
(residue number reindexed from 1)		M17 W29 L35 A44 I50 L51 C53 K54 R58 Q75 V77 L138 Y140
Annotation score1
Binding affinityMOAD: Kd=10nM
BindingDB: Kd=10.0nM
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:4jvf, PDBe:4jvf, PDBj:4jvf
PDBsum4jvf
PubMed23698361
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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