2P2I

Crystal structure of the VEGFR2 kinase domain in complex with a nicotinamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Evolution of a Highly Selective and Potent 2-(Pyridin-2-yl)-1,3,5-triazine Tie-2 Kinase Inhibitor

Hodous, B.L.Geuns-Meyer, S.D.Hughes, P.E.Albrecht, B.K.Bellon, S.Bready, J.Caenepeel, S.Cee, V.J.Chaffee, S.C.Coxon, A.Emery, M.Fretland, J.Gallant, P.Gu, Y.Hoffman, D.Johnson, R.E.Kendall, R.Kim, J.L.Long, A.M.Morrison, M.Olivieri, P.R.Patel, V.F.Polverino, A.Rose, P.Tempest, P.Wang, L.Whittington, D.A.Zhao, H.

(2007) J.Med.Chem. 50: 611-626

  • DOI: 10.1021/jm061107l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of angiogenesis is a promising and clinically validated approach for limiting tumor growth and survival. The receptor tyrosine kinase Tie-2 is expressed almost exclusively in the vascular endothelium and is required for developmental angio ...

    Inhibition of angiogenesis is a promising and clinically validated approach for limiting tumor growth and survival. The receptor tyrosine kinase Tie-2 is expressed almost exclusively in the vascular endothelium and is required for developmental angiogenesis and vessel maturation. However, the significance of Tie-2 signaling in tumor angiogenesis is not well understood. In order to evaluate the therapeutic utility of inhibiting Tie-2 signaling, we developed a series of potent and orally bioavailable small molecule Tie-2 kinase inhibitors with selectivity over other kinases, especially those that are believed to be important for tumor angiogenesis. Our earlier work provided pyridinyl pyrimidine 6 as a potent, nonselective Tie-2 inhibitor that was designed on the basis of X-ray cocrystal structures of KDR inhibitors 34 (triazine) and 35 (nicotinamide). Lead optimization resulted in pyridinyl triazine 63, which exhibited >30-fold selectivity over a panel of kinases, good oral exposure, and in vivo inhibition of Tie-2 phosphorylation.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139-1581, USA. bhodous@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A, B
314Homo sapiensMutation(s): 2 
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
608
Query on 608

Download SDF File 
Download CCD File 
A, B
N-(4-phenoxyphenyl)-2-[(pyridin-4-ylmethyl)amino]nicotinamide
C24 H20 N4 O2
CPVRYQAOUPSUDO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
608Ki: 10 nM (85) BINDINGDB
608IC50: 38 nM (85) BINDINGDB
608IC50: 38 nM BINDINGMOAD
608IC50: 38 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.420α = 90.00
b = 67.060β = 94.51
c = 88.510γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-16
    Type: Refinement description, Source and taxonomy