Structure of PDB 6d5e Chain B Binding Site BS01

Receptor Information
>6d5e 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 IDFVG
InChIInChI=1S/C25H32ClFN6/c1-16-10-18(11-17(2)23(16)27)15-33-22-13-19(26)12-21(32-7-3-4-20(32)14-28)24(22)30-25(33)31-8-5-29-6-9-31/h10-13,20,29H,3-9,14-15,28H2,1-2H3/t20-/m0/s1
InChIKeyCAPZSPOPEHSYOZ-FQEVSTJZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(Cn2c3cc(Cl)cc(N4CCC[C@H]4CN)c3nc2N5CCNCC5)cc(C)c1F
CACTVS 3.385Cc1cc(Cn2c3cc(Cl)cc(N4CCC[CH]4CN)c3nc2N5CCNCC5)cc(C)c1F
ACDLabs 12.01n4c2c(N1C(CCC1)CN)cc(cc2n(Cc3cc(c(c(C)c3)F)C)c4N5CCNCC5)Cl
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1F)C)Cn2c3cc(cc(c3nc2N4CCNCC4)N5CCCC5CN)Cl
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1F)C)Cn2c3cc(cc(c3nc2N4CCNCC4)N5CCC[C@H]5CN)Cl
FormulaC25 H32 Cl F N6
Name1-[(2S)-1-{6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazol-4-yl}pyrrolidin-2-yl]methanamine
ChEMBLCHEMBL4215257
DrugBank
ZINC
PDB chain6d5e 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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PDB6d5e Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		M878 N879 V883 Y884 D887 F890 L901 H905
Binding residue
(residue number reindexed from 1)		M301 N302 V306 Y307 D310 F313 L324 H328
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.85,Kd=0.14uM
BindingDB: Kd=140nM,EC50=3200nM
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:6d5e, PDBe:6d5e, PDBj:6d5e
PDBsum6d5e
PubMed30205005
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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