Structure of PDB 3vid Chain A Binding Site BS01

Receptor Information
>3vid Chain A (length=299) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATC
RTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPL
MVIVEFCKFGNLSTYLRSKRNEFVPYKEAPEDLYKDFLTLEHLICYSFQV
AKGMEFLASRKCIHRDLAARNILLSEKNVVKICDYKDPDYVRKGDARLPL
KWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRL
KEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA
Ligand information
Ligand ID4TT
InChIInChI=1S/C14H13N3/c1-2-7-12-10(5-1)11-6-3-4-9-8-15-17-13(9)14(11)16-12/h1-2,5,7-8,16H,3-4,6H2,(H,15,17)
InChIKeyHBWXPQZQCDQNND-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C1Cc2cn[nH]c2c3[nH]c4ccccc4c3C1
OpenEye OEToolkits 1.7.2c1ccc2c(c1)c3c([nH]2)-c4c(cn[nH]4)CCC3
ACDLabs 12.01n4cc3c(c2c(c1ccccc1n2)CCC3)n4
FormulaC14 H13 N3
Name4,5,6,11-tetrahydro-1H-pyrazolo[4',3':6,7]cyclohepta[1,2-b]indole
ChEMBLCHEMBL1929485
DrugBank
ZINCZINC000082155336
PDB chain3vid 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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PDB3vid A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		V848 A866 E917 F918 C919 G922 L1035
Binding residue
(residue number reindexed from 1)		V36 A54 E105 F106 C107 G110 L173
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.21,IC50=620nM
Enzymatic activity
Catalytic site (original residue number in PDB) D1028 R1032 N1033 D1046 K1055
Catalytic site (residue number reindexed from 1) D166 R170 N171 D184 K186
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:3vid, PDBe:3vid, PDBj:3vid
PDBsum3vid
PubMed24900475
UniProtP35968|VGFR2_HUMAN Vascular endothelial growth factor receptor 2 (Gene Name=KDR)

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