Structure of PDB 3vnt Chain A Binding Site BS01

Receptor Information
>3vnt Chain A (length=301) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTAT
CRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGP
LMVIVEFCKFGNLSTYLRSKRNEFVPYKYKDFLTLEHLICYSFQVAKGME
FLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARL
PLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCR
RLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQAN
A
Ligand information
Ligand ID0JA
InChIInChI=1S/C27H19ClFN5O3S/c28-22-16(2-1-3-17(22)27(13-30)10-11-27)24(36)31-20-12-15(6-7-18(20)29)37-21-9-8-19-25(33-21)38-26(32-19)34-23(35)14-4-5-14/h1-3,6-9,12,14H,4-5,10-11H2,(H,31,36)(H,32,34,35)
InChIKeyMDPMAXSABUPRJI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Fc1ccc(Oc2ccc3nc(NC(=O)C4CC4)sc3n2)cc1NC(=O)c5cccc(c5Cl)C6(CC6)C#N
ACDLabs 12.01N#CC6(c1cccc(c1Cl)C(=O)Nc5c(F)ccc(Oc2nc3sc(nc3cc2)NC(=O)C4CC4)c5)CC6
OpenEye OEToolkits 1.7.6c1cc(c(c(c1)C2(CC2)C#N)Cl)C(=O)Nc3cc(ccc3F)Oc4ccc5c(n4)sc(n5)NC(=O)C6CC6
FormulaC27 H19 Cl F N5 O3 S
Name2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]benzamide
ChEMBLCHEMBL2063743
DrugBank
ZINCZINC000059083294
PDB chain3vnt Chain A Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vnt Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors. 1. Exploration of [5,6]-fused bicyclic scaffolds
Resolution1.64 Å
Binding residue
(original residue number in PDB)		V848 A866 K868 E885 L889 I892 V898 V899 V916 F918 C919 K920 G922 L1019 L1035 C1045 D1046 F1047
Binding residue
(residue number reindexed from 1)		V37 A55 K57 E74 L78 I81 V87 V88 V105 F107 C108 K109 G111 L152 L168 C178 D179 F180
Annotation score1
Binding affinityMOAD: ic50=2.2nM
PDBbind-CN: -logKd/Ki=8.66,IC50=2.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 A1030 R1032 N1033 D1046 K1055
Catalytic site (residue number reindexed from 1) D161 A163 R165 N166 D179 K188
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:3vnt, PDBe:3vnt, PDBj:3vnt
PDBsum3vnt
PubMed22376051
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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