Structure of PDB 4nyj Chain S Binding Site BS01

Receptor Information
>4nyj Chain S (length=468) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QMRLPSADVYRFAEPDSEENIIFEEGIPIIKAGTVIKLIERLTYHMYADP
NFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLS
AELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTV
RGKAMKKWVESITKIIQRKKIANITFQSSPPTVEWHISRPGHIETFDLLT
LHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHT
TNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAM
NSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVP
FFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQP
YCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFP
KKYSYPLKSPGVRPSNPR
Ligand information
Ligand ID2PZ
InChIInChI=1S/C16H22N4O/c17-9-16(21)19-13-5-7-20(8-6-13)11-12-10-18-15-4-2-1-3-14(12)15/h1-4,10,13,18H,5-9,11,17H2,(H,19,21)
InChIKeyCVIHXVZLCLPGPP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC3CCN(Cc1cnc2ccccc12)CC3)CN
CACTVS 3.385NCC(=O)NC1CCN(CC1)Cc2c[nH]c3ccccc23
OpenEye OEToolkits 1.7.6c1ccc2c(c1)c(c[nH]2)CN3CCC(CC3)NC(=O)CN
FormulaC16 H22 N4 O
NameN-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]glycinamide
ChEMBLCHEMBL4169930
DrugBank
ZINCZINC000098208233
PDB chain4nyj 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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PDB4nyj Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Resolution2.8522 Å
Binding residue
(original residue number in PDB)		M878 N879 Y884 F890
Binding residue
(residue number reindexed from 1)		M300 N301 Y306 F312
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.49,Kd=322uM
BindingDB: EC50=>100000nM
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
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Biological Process
External links
PDB RCSB:4nyj, PDBe:4nyj, PDBj:4nyj
PDBsum4nyj
PubMed24550516
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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