1YWN

Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors

Miyazaki, Y.Matsunaga, S.Tang, J.Maeda, Y.Nakano, M.Philippe, R.J.Shibahara, M.Liu, W.Sato, H.Wang, L.Nolte, R.T.

(2005) Bioorg.Med.Chem.Lett. 15: 2203-2207

  • DOI: 10.1016/j.bmcl.2005.03.034

  • PubMed Abstract: 
  • A novel class of furo[2,3-d]pyrimidines has been discovered as potent dual inhibitors of Tie-2 and VEGFR2 receptor tyrosine kinases (TK) and a diarylurea moiety at 5-position shows remarkably enhanced activity against both enzymes. One of the most ac ...

    A novel class of furo[2,3-d]pyrimidines has been discovered as potent dual inhibitors of Tie-2 and VEGFR2 receptor tyrosine kinases (TK) and a diarylurea moiety at 5-position shows remarkably enhanced activity against both enzymes. One of the most active compounds, 4-amino-3-(4-((2-fluoro-5-(trifluoromethyl)phenyl)amino-carbonylamino)phenyl)-2-(4-methoxyphenyl)furo[2,3-d]pyrimidine (7k) is <3 nM on both TK receptors and the activity is rationalized based on the X-ray crystal structure.


    Organizational Affiliation

    GlaxoSmithKline K.K., Tsukuba Research Laboratories, 43, Wadai, Tsukuba 300-4247, Ibaraki, Japan. yasushi.miyazaki@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A
316Homo sapiensMutation(s): 1 
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
LIF
Query on LIF

Download SDF File 
Download CCD File 
A
N-{4-[4-AMINO-6-(4-METHOXYPHENYL)FURO[2,3-D]PYRIMIDIN-5-YL]PHENYL}-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA
N-(4-{4-AMINO-6-[4-(METHYLOXY)PHENYL]FURO[2,3-D]PYRIMIDIN-5-YL}PHENYL)-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA
C27 H19 F4 N5 O3
FGZIONRFHVNRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LIFIC50: 3 - 15.5 nM (86) BINDINGDB
LIFIC50: ~3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.953α = 90.00
b = 95.595β = 90.00
c = 95.803γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MAR345data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description