Structure of PDB 6d5w Chain S Binding Site BS01

Receptor Information
>6d5w Chain S (length=469) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QMRLPSADVYRFAEPDSEENIIFEEGIPIIKAGTVIKLIERLTYHMYADP
NFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLS
AELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTV
RGKAMKKWVESITKIIQRKKIAHNITFQSSPPTVEWHISRPGHIETFDLL
TLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRH
TTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSA
MNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCV
PFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQ
PYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRF
PKKYSYPLKSPGVRPSNPR
Ligand information
Ligand IDFVV
InChIInChI=1S/C17H16FN3/c18-14-8-6-13(7-9-14)12-21-16-5-2-1-4-15(16)20-11-3-10-19-17(20)21/h1-2,4-9H,3,10-12H2
InChIKeyLXOFDRFYSDHQTI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1ccc(CN2c3ccccc3N4CCCN=C24)cc1
ACDLabs 12.01c4(ccc(CN3C=1N(CCCN=1)c2c3cccc2)cc4)F
OpenEye OEToolkits 2.0.6c1ccc2c(c1)N3CCCN=C3N2Cc4ccc(cc4)F
FormulaC17 H16 F N3
Name10-[(4-fluorophenyl)methyl]-2,3,4,10-tetrahydropyrimido[1,2-a]benzimidazole
ChEMBLCHEMBL1624889
DrugBank
ZINCZINC000004334103
PDB chain6d5w Chain S Residue 1101 [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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PDB6d5w Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Resolution2.478 Å
Binding residue
(original residue number in PDB)		V852 V883 Y884 F890 L901
Binding residue
(residue number reindexed from 1)		V275 V306 Y307 F313 L324
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.20,IC50=63.0uM
BindingDB: EC50=63000nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005085 guanyl-nucleotide exchange factor activity
Biological Process
GO:0007264 small GTPase-mediated signal transduction

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Molecular Function
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Biological Process
External links
PDB RCSB:6d5w, PDBe:6d5w, PDBj:6d5w
PDBsum6d5w
PubMed30205005
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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