Structure of PDB 4nyi Chain S Binding Site BS01

Receptor Information
>4nyi Chain S (length=472) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QMRLPSADVYRFAEPDSEENIIFEENMAGIPIIKAGTVIKLIERLTYHMY
ADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQ
PLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFI
GTVRGKAMKKWVESITKIIQRKKIAHNITFQSSPPTVEWHISRPGHIETF
DLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKM
IRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEV
VSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINP
PCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQY
QNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPL
PRFPKKYSYPLKSPGVRPSNPR
Ligand information
Ligand ID2PX
InChIInChI=1S/C26H31N5O/c1-17-6-7-25-22(12-17)19(15-29-25)16-31-10-8-20(9-11-31)30-26(32)23(27)13-18-14-28-24-5-3-2-4-21(18)24/h2-7,12,14-15,20,23,28-29H,8-11,13,16,27H2,1H3,(H,30,32)/t23-/m0/s1
InChIKeyHAGXHOXTZOWANA-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc2[nH]cc(CN3CCC(CC3)NC(=O)[CH](N)Cc4c[nH]c5ccccc45)c2c1
OpenEye OEToolkits 1.7.6Cc1ccc2c(c1)c(c[nH]2)CN3CCC(CC3)NC(=O)[C@H](Cc4c[nH]c5c4cccc5)N
ACDLabs 12.01O=C(NC3CCN(Cc1cnc2ccc(cc12)C)CC3)C(N)Cc5c4ccccc4nc5
OpenEye OEToolkits 1.7.6Cc1ccc2c(c1)c(c[nH]2)CN3CCC(CC3)NC(=O)C(Cc4c[nH]c5c4cccc5)N
CACTVS 3.385Cc1ccc2[nH]cc(CN3CCC(CC3)NC(=O)[C@@H](N)Cc4c[nH]c5ccccc45)c2c1
FormulaC26 H31 N5 O
NameN-{1-[(5-methyl-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide
ChEMBLCHEMBL4166974
DrugBank
ZINCZINC000098208232
PDB chain4nyi Chain S Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nyi Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Resolution2.9612 Å
Binding residue
(original residue number in PDB)		M878 Y884 F890 K898 L901
Binding residue
(residue number reindexed from 1)		M304 Y310 F316 K324 L327
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.06,Kd=868uM
BindingDB: EC50=25100nM
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:4nyi, PDBe:4nyi, PDBj:4nyi
PDBsum4nyi
PubMed24550516
UniProtQ07889|SOS1_HUMAN Son of sevenless homolog 1 (Gene Name=SOS1)

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