Structure of PDB 6d5h Chain B Binding Site BS01

Receptor Information
>6d5h Chain B (length=469) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQMRLPSADVYRFAEPDSEENIIFEEGIPIIKAGTVIKLIERLTYHMYAD
PNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPL
SAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGT
VRGKAMKKWVESITKIIQRKKIANITFQSSPPTVEWHISRPGHIETFDLL
TLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRH
TTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSA
MNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCV
PFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQ
PYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRF
PKKYSYPLKSPGVRPSNPR
Ligand information
Ligand IDFV7
InChIInChI=1S/C26H25Cl2FN4/c1-16-11-18(12-17(2)24(16)29)15-33-23-14-19(27)13-21(20-5-3-4-6-22(20)28)25(23)31-26(33)32-9-7-30-8-10-32/h3-6,11-14,30H,7-10,15H2,1-2H3
InChIKeyYIYWIIQFTVKZTC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1F)C)Cn2c3cc(cc(c3nc2N4CCNCC4)c5ccccc5Cl)Cl
ACDLabs 12.01n4c2c(c1ccccc1Cl)cc(cc2n(Cc3cc(C)c(F)c(c3)C)c4N5CCNCC5)Cl
CACTVS 3.385Cc1cc(Cn2c3cc(Cl)cc(c4ccccc4Cl)c3nc2N5CCNCC5)cc(C)c1F
FormulaC26 H25 Cl2 F N4
Name6-chloro-4-(2-chlorophenyl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
ChEMBLCHEMBL4214176
DrugBank
ZINC
PDB chain6d5h Chain B Residue 2001 [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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PDB6d5h Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		M878 N879 V883 Y884 D887 F890 L901 E902
Binding residue
(residue number reindexed from 1)		M301 N302 V306 Y307 D310 F313 L324 E325
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM
BindingDB: EC50=11000nM,Kd=120nM
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:6d5h, PDBe:6d5h, PDBj:6d5h
PDBsum6d5h
PubMed30205005
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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