5EW3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5EW3

  • 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 assays, the compounds exhibit single-digit nanomolar potency toward VEGFR2 ...

    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) Biochim Biophys Acta 1697: 17

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2A, B316Homo sapiensMutation(s): 0 
Gene Names: KDRFLK1VEGFR2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5T2 (Subject of Investigation/LOI)
Query on 5T2

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide
C20 H16 F3 N3 O
BLAFVGLBBOPRLP-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5T2 BindingDB:  5EW3 IC50: min: 1.2, max: 170 (nM) from 7 assay(s)
Binding MOAD:  5EW3 IC50: 1.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.5α = 90
b = 55.76β = 92.28
c = 89.76γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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