Structure of PDB 6d56 Chain B Binding Site BS01

Receptor Information
>6d56 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 IDFVM
InChIInChI=1S/C26H28ClFN6/c1-14-5-18(6-15(2)23(14)28)9-34-21-8-19(27)7-20(22-16(3)31-32-17(22)4)24(21)30-25(34)33-12-26(13-33)10-29-11-26/h5-8,29H,9-13H2,1-4H3,(H,31,32)
InChIKeyWYYRAJGTUGUYGY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]nc(C)c1c2cc(Cl)cc3n(Cc4cc(C)c(F)c(C)c4)c(nc23)N5CC6(CNC6)C5
ACDLabs 12.01n4c2c(c1c(C)nnc1C)cc(cc2n(Cc3cc(C)c(c(C)c3)F)c4N6CC5(CNC5)C6)Cl
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1F)C)Cn2c3cc(cc(c3nc2N4CC5(C4)CNC5)c6c([nH]nc6C)C)Cl
FormulaC26 H28 Cl F N6
Name6-chloro-2-(2,6-diazaspiro[3.3]heptan-2-yl)-4-(3,5-dimethyl-1H-pyrazol-4-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-1H-benzimidazole
ChEMBLCHEMBL4214703
DrugBank
ZINC
PDB chain6d56 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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PDB6d56 Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		V875 M878 N879 V883 Y884 L886 D887 F890 L901 E902 H905
Binding residue
(residue number reindexed from 1)		V298 M301 N302 V306 Y307 L309 D310 F313 L324 E325 H328
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.05,Kd=0.009uM
BindingDB: EC50=21100nM,Kd=9.0nM
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:6d56, PDBe:6d56, PDBj:6d56
PDBsum6d56
PubMed30205005
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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