Structure of PDB 6jok Chain A Binding Site BS01

Receptor Information
>6jok Chain A (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFG
KVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHL
NIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHEVKNLLSDD
NSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKIC
DFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILL
WEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNS
EPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD
Ligand information
Ligand IDB49
InChIInChI=1S/C22H27FN4O2/c1-5-27(6-2)10-9-24-22(29)20-13(3)19(25-14(20)4)12-17-16-11-15(23)7-8-18(16)26-21(17)28/h7-8,11-12,25H,5-6,9-10H2,1-4H3,(H,24,29)(H,26,28)/b17-12-
InChIKeyWINHZLLDWRZWRT-ATVHPVEESA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCN(CC)CCNC(=O)c1c(C)[nH]c(/C=C/2C(=O)Nc3ccc(F)cc/23)c1C
OpenEye OEToolkits 1.7.2CCN(CC)CCNC(=O)c1c(c([nH]c1C)/C=C\2/c3cc(ccc3NC2=O)F)C
OpenEye OEToolkits 1.7.2CCN(CC)CCNC(=O)c1c(c([nH]c1C)C=C2c3cc(ccc3NC2=O)F)C
ACDLabs 12.01O=C(NCCN(CC)CC)c1c(c(nc1C)/C=C3/c2cc(F)ccc2NC3=O)C
CACTVS 3.370CCN(CC)CCNC(=O)c1c(C)[nH]c(C=C2C(=O)Nc3ccc(F)cc23)c1C
FormulaC22 H27 F N4 O2
NameN-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide;
SUNITINIB
ChEMBLCHEMBL535
DrugBankDB01268
ZINCZINC000003964325
PDB chain6jok Chain A Residue 1001 [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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PDB6jok Crystal structure of PDGFRA in complex with sunitinib by soaking
Resolution3.8 Å
Binding residue
(original residue number in PDB)		L599 V607 A625 K627 V658 T674 E675 C677 F678 G680 N684 L825
Binding residue
(residue number reindexed from 1)		L44 V52 A70 K72 V103 T119 E120 C122 F123 G125 N129 L190
Annotation score1
Binding affinityBindingDB: Kd=0.790000nM,IC50=130nM
Enzymatic activity
Catalytic site (original residue number in PDB) D818 R822 N823 D836
Catalytic site (residue number reindexed from 1) D183 R187 N188 D201
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6jok, PDBe:6jok, PDBj:6jok
PDBsum6jok
PubMed
UniProtP16234|PGFRA_HUMAN Platelet-derived growth factor receptor alpha (Gene Name=PDGFRA)

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