Structure of PDB 4ag8 Chain A Binding Site BS01

Receptor Information
>4ag8 Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTV
AVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVI
VEFCKFGNLSTYLRSKRNEFVPYYKDFLTLEHLICYSFQVAKGMEFLASR
KCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWM
APETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEG
TRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA
Ligand information
Ligand IDAXI
InChIInChI=1S/C22H18N4OS/c1-23-22(27)18-7-2-3-8-21(18)28-16-10-11-17-19(25-26-20(17)14-16)12-9-15-6-4-5-13-24-15/h2-14H,1H3,(H,23,27)(H,25,26)/b12-9+
InChIKeyRITAVMQDGBJQJZ-FMIVXFBMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)c1ccccc1Sc2ccc3c([nH]nc3C=Cc4ccccn4)c2
CACTVS 3.385CNC(=O)c1ccccc1Sc2ccc3c([nH]nc3\C=C\c4ccccn4)c2
OpenEye OEToolkits 2.0.7CNC(=O)c1ccccc1Sc2ccc3c(c2)[nH]nc3/C=C/c4ccccn4
ACDLabs 12.01O=C(NC)c4ccccc4Sc2ccc3c(\C=C\c1ncccc1)nnc3c2
OpenEye OEToolkits 2.0.7CNC(=O)c1ccccc1Sc2ccc3c(c2)[nH]nc3C=Cc4ccccn4
FormulaC22 H18 N4 O S
NameAXITINIB;
N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL-VINYL)-1H-INDAZOL-6-YLSULFANYL)-BENZAMIDE
ChEMBLCHEMBL1289926
DrugBankDB06626
ZINCZINC000003816287
PDB chain4ag8 Chain A Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ag8 Molecular Conformations, Interactions, and Properties Associated with Drug Efficiency and Clinical Performance Among Vegfr Tk Inhibitors.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		V848 A866 K868 E885 V914 V916 F918 C919 K920 G922 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V33 A51 K53 E70 V99 V101 F103 C104 K105 G107 L163 C173 D174 F175
Annotation score1
Binding affinityMOAD: Ki=1.1nM
PDBbind-CN: -logKd/Ki=8.96,Ki=1.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 K1055 D1064
Catalytic site (residue number reindexed from 1) D156 A158 R160 N161 D174 K183 D192
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:4ag8, PDBe:4ag8, PDBj:4ag8
PDBsum4ag8
PubMed22988103
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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