5EW3

Human Vascular Endothelial Growth Factor Receptor 2 (KDR) Kinase Domain in complex with AAL993


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Novel Potent Oral Series of VEGFR2 Inhibitors Abrogate Tumor Growth by Inhibiting Angiogenesis.

Bold, G.Schnell, C.Furet, P.McSheehy, P.Bruggen, J.Mestan, J.Manley, P.W.Druckes, P.Burglin, M.Durler, U.Loretan, J.Reuter, R.Wartmann, M.Theuer, A.Bauer-Probst, B.Martiny-Baron, G.Allegrini, P.Goepfert, A.Wood, J.Littlewood-Evans, A.

(2016) J.Med.Chem. 59: 132-146

  • DOI: 10.1021/acs.jmedchem.5b01582

  • PubMed Abstract: 
  • This paper describes the identification of 6-(pyrimidin-4-yloxy)-naphthalene-1-carboxamides as a new class of potent and selective human vascular endothelial growth factor receptor 2 (VEGFR2) tyrosine kinase inhibitors. In biochemical and cellular as ...

    This paper describes the identification of 6-(pyrimidin-4-yloxy)-naphthalene-1-carboxamides as a new class of potent and selective human vascular endothelial growth factor receptor 2 (VEGFR2) tyrosine kinase inhibitors. In biochemical and cellular assays, the compounds exhibit single-digit nanomolar potency toward VEGFR2. Compounds of this series show good exposure in rodents when dosed orally. They potently inhibit VEGF-driven angiogenesis in a chamber model and rodent tumor models at daily doses of less than 3 mg/kg by targeting the tumor vasculature as demonstrated by ELISA for TIE-2 in lysates or by immunohistochemical analysis. This novel series of compounds shows a potential for the treatment of solid tumors and other diseases where angiogenesis plays an important role.


    Related Citations: 
    • Advances in the structural biology, design and clinical development of VEGF-R kinase inhibitors for the treatment of angiogenesis
      Manley, P.W.,Bold, G.,Bruggen, J.,Fendrich, G.,Furet, P.,Mestan, J.,Schnell, C.,Stolz, B.,Meyer, T.,Meyhack, B.,Stark, W.,Strauss, A.,Wood, J.
      (2004) Biochimica et Biophysica Acta, Proteins and Proteomics 1697: 17


    Organizational Affiliation

    Oncology Research, Novartis Institutes for BioMedical Research , 4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A, B
316Homo sapiensMutation(s): 0 
Gene Names: KDR (FLK1, VEGFR2)
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Go to Gene View: KDR
Go to UniProtKB:  P35968
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5T2
Query on 5T2

Download SDF File 
Download CCD File 
A, B
2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide
C20 H16 F3 N3 O
BLAFVGLBBOPRLP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5T2IC50: 1.2 - 170 nM (86) BINDINGDB
5T2IC50: 1.2 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.500α = 90.00
b = 55.760β = 92.28
c = 89.760γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
AMoREphasing
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references