Structure of PDB 6d5g Chain B Binding Site BS01

Receptor Information
>6d5g 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 IDFVD
InChIInChI=1S/C25H29ClFN5/c1-16-11-18(12-17(2)23(16)27)15-32-22-14-20(26)13-21(19-3-5-28-6-4-19)24(22)30-25(32)31-9-7-29-8-10-31/h3,11-14,28-29H,4-10,15H2,1-2H3
InChIKeyAICGXPKTEXWHDK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(Cn2c3cc(Cl)cc(C4=CCNCC4)c3nc2N5CCNCC5)cc(C)c1F
ACDLabs 12.01n3(c2cc(cc(C=1CCNCC=1)c2nc3N4CCNCC4)Cl)Cc5cc(C)c(c(c5)C)F
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1F)C)Cn2c3cc(cc(c3nc2N4CCNCC4)C5=CCNCC5)Cl
FormulaC25 H29 Cl F N5
Name6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole
ChEMBLCHEMBL4205543
DrugBank
ZINC
PDB chain6d5g 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6d5g Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		M878 N879 V883 Y884 D887 F890 L901 E902 H905
Binding residue
(residue number reindexed from 1)		M301 N302 V306 Y307 D310 F313 L324 E325 H328
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.60,Kd=0.25uM
BindingDB: Kd=250nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6d5g, PDBe:6d5g, PDBj:6d5g
PDBsum6d5g
PubMed30205005
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

[Back to BioLiP]