Structure of PDB 3cjf Chain A Binding Site BS01

Receptor Information
>3cjf Chain A (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CERLPYDASKWEFPRDRLNLGKPLGRGAFGQVIEADAFGIDKTATCRTVA
VKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIV
EFCKFGNLSTYLRSKRNEFVPYKKDFLTLEHLICYSFQVAKGMEFLASRK
CIHRDLAARNILLSEKNVVKICDLARDIYKPLKWMAPETIFDRVYTIQSD
VWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQ
TMLDCWHGEPSQRPTFSELVEHLGNLLQANA
Ligand information
Ligand IDSAV
InChIInChI=1S/C21H22N6O3/c1-12-15-6-5-13(9-16(15)27-26-12)23-19-7-8-22-21(25-19)24-14-10-17(28-2)20(30-4)18(11-14)29-3/h5-11H,1-4H3,(H,26,27)(H2,22,23,24,25)
InChIKeySQQAPOSROFWHIB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COc1cc(Nc2nccc(Nc3ccc4c([nH]nc4C)c3)n2)cc(OC)c1OC
OpenEye OEToolkits 1.5.0Cc1c2ccc(cc2[nH]n1)Nc3ccnc(n3)Nc4cc(c(c(c4)OC)OC)OC
ACDLabs 10.04O(c1cc(cc(OC)c1OC)Nc2nccc(n2)Nc3ccc4c(c3)nnc4C)C
FormulaC21 H22 N6 O3
NameN~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
ChEMBLCHEMBL479079
DrugBankDB08519
ZINCZINC000004617990
PDB chain3cjf Chain A Residue 1167 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cjf Discovery of 5-[[4-[(2,3-dimethyl-2H-indazol-6-yl)methylamino]-2-pyrimidinyl]amino]-2-methyl-benzenesulfonamide (Pazopanib), a novel and potent vascular endothelial growth factor receptor inhibitor.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		L838 A864 F916 C917 K918 G920 L1033
Binding residue
(residue number reindexed from 1)		L24 A50 F102 C103 K104 G106 L162
Annotation score1
Binding affinityMOAD: ic50=6.3nM
PDBbind-CN: -logKd/Ki=8.20,IC50=6.3nM
BindingDB: IC50=6.3nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1026 A1028 R1030 N1031 D1044 K1053
Catalytic site (residue number reindexed from 1) D155 A157 R159 N160 D173 K180
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3cjf, PDBe:3cjf, PDBj:3cjf
PDBsum3cjf
PubMed18620382
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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