2RL5

Crystal structure of the VEGFR2 kinase domain in complex with a 2,3-dihydro-1,4-benzoxazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis.

La, D.S.Belzile, J.Bready, J.V.Coxon, A.Demelfi, T.Doerr, N.Estrada, J.Flynn, J.C.Flynn, S.R.Graceffa, R.F.Harriman, S.P.Larrow, J.F.Long, A.M.Martin, M.W.Morrison, M.J.Patel, V.F.Roveto, P.M.Wang, L.Weiss, M.M.Whittington, D.A.Teffera, Y.Zhao, Z.Polverino, A.J.Harmange, J.C.

(2008) J Med Chem 51: 1695-1705

  • DOI: 10.1021/jm701129j
  • Primary Citation of Related Structures:  
    2RL5

  • PubMed Abstract: 
  • Angiogenesis is vital for solid tumor growth, and its prevention is a proven strategy for the treatment of disease states such as cancer. The vascular endothelial growth factor (VEGF) pathway provides several opportunities by which small molecules can ac ...

    Angiogenesis is vital for solid tumor growth, and its prevention is a proven strategy for the treatment of disease states such as cancer. The vascular endothelial growth factor (VEGF) pathway provides several opportunities by which small molecules can act as inhibitors of endothelial proliferation and migration. Critical to these processes is signaling through VEGFR-2 or the kinase insert domain receptor (KDR) upon stimulation by its ligand VEGF. Herein, we report the discovery of 2,3-dihydro-1,4-benzoxazines as inhibitors of intrinsic KDR activity (IC 50 < 0.1 microM) and human umbilical vein endothelial cell (HUVEC) proliferation with IC 50 < 0.1 microM. More specifically, compound 16 was identified as a potent (KDR: < 1 nM and HUVEC: 4 nM) and selective inhibitor that exhibited efficacy in angiogenic in vivo models. In addition, this series of molecules is typically well-absorbed orally, further demonstrating the 2,3-dihydro-1,4-benzoxazine moiety as a promising platform for generating kinase-based antiangiogenic therapeutic agents.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA. daniel.la@amgen.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2 A314Homo sapiensMutation(s): 3 
Gene Names: KDRFLK1
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
NIH Common Fund Data Resources
PHAROS:  P35968
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2RL
Query on 2RL

Download Ideal Coordinates CCD File 
A
N-(4-CHLOROPHENYL)-7-[(6,7-DIMETHOXYQUINOLIN-4-YL)OXY]-2,3-DIHYDRO-1,4-BENZOXAZINE-4-CARBOXAMIDE
C26 H22 Cl N3 O5
RNHWXYKRVZUXGO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2RLIC50:  0.5   nM  BindingDB
2RLIC50 :  4   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.76α = 90
b = 139.774β = 90
c = 57.55γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.3: 2019-11-13
    Changes: Structure summary