Structure of PDB 4asd Chain A Binding Site BS01

Receptor Information
>4asd Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGI
DKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACT
KPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYYKDFLTLEHLICYSFQVA
KGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKG
DARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDE
EFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNL
LQANA
Ligand information
Ligand IDBAX
InChIInChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
InChIKeyMLDQJTXFUGDVEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c3nccc(Oc2ccc(NC(=O)Nc1ccc(Cl)c(c1)C(F)(F)F)cc2)c3)NC
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
CACTVS 3.341CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
FormulaC21 H16 Cl F3 N4 O3
Name4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE;
Sorafenib
ChEMBLCHEMBL1336
DrugBankDB00398
ZINCZINC000001493878
PDB chain4asd Chain A Residue 1500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4asd Molecular Conformations, Interactions, and Properties Associated with Drug Efficiency and Clinical Performance Among Vegfr Tk Inhibitors.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		L840 V848 A866 K868 E885 L889 V916 E917 F918 C919 G922 L1019 L1035 I1044 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		L34 V42 A60 K62 E79 L83 V110 E111 F112 C113 G116 L156 L172 I181 C182 D183 F184
Annotation score1
Binding affinityMOAD: Ki=0.52nM
PDBbind-CN: -logKd/Ki=9.28,Ki=0.52nM
BindingDB: IC50=90nM,Kd=59nM,Ki=22nM,EC50=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 D1064
Catalytic site (residue number reindexed from 1) D165 A167 R169 N170 D183 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

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Molecular Function
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Biological Process
External links
PDB RCSB:4asd, PDBe:4asd, PDBj:4asd
PDBsum4asd
PubMed22988103
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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