Structure of PDB 4nym Chain S Binding Site BS01

Receptor Information
>4nym Chain S (length=469) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QMRLPSADVYRFAEPDSEENIIFEEGIPIIKAGTVIKLIERLTYHMYADP
NFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLS
AELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTV
RGKAMKKWVESITKIIQRKKIAHNITFQSSPPTVEWHISRPGHIETFDLL
TLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRH
TTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSA
MNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCV
PFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQ
PYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRF
PKKYSYPLKSPGVRPSNPR
Ligand information
Ligand IDRND
InChIInChI=1S/C25H29N5O/c26-22(13-17-14-27-23-7-3-1-5-20(17)23)25(31)29-19-9-11-30(12-10-19)16-18-15-28-24-8-4-2-6-21(18)24/h1-8,14-15,19,22,27-28H,9-13,16,26H2,(H,29,31)/t22-/m0/s1
InChIKeyYLGBZXMOCLUOKZ-QFIPXVFZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[C@@H](Cc1c[nH]c2ccccc12)C(=O)NC3CCN(CC3)Cc4c[nH]c5ccccc45
OpenEye OEToolkits 1.7.6c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NC3CCN(CC3)Cc4c[nH]c5c4cccc5)N
ACDLabs 12.01O=C(NC3CCN(Cc1cnc2ccccc12)CC3)C(N)Cc5c4ccccc4nc5
CACTVS 3.385N[CH](Cc1c[nH]c2ccccc12)C(=O)NC3CCN(CC3)Cc4c[nH]c5ccccc45
OpenEye OEToolkits 1.7.6c1ccc2c(c1)c(c[nH]2)CC(C(=O)NC3CCN(CC3)Cc4c[nH]c5c4cccc5)N
FormulaC25 H29 N5 O
NameN-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide
ChEMBLCHEMBL4172691
DrugBank
ZINCZINC000098209370
PDB chain4nym 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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PDB4nym Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Resolution3.5529 Å
Binding residue
(original residue number in PDB)		M878 Y884 F890 K898 E902 H905
Binding residue
(residue number reindexed from 1)		M301 Y307 F313 K321 E325 H328
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.55,Kd=279uM
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:4nym, PDBe:4nym, PDBj:4nym
PDBsum4nym
PubMed24550516
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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