3VHE

Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report



Literature

Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase conformation.

Oguro, Y.Miyamoto, N.Okada, K.Takagi, T.Iwata, H.Awazu, Y.Miki, H.Hori, A.Kamiyama, K.Imamura, S.

(2010) Bioorg Med Chem 18: 7260-7273

  • DOI: 10.1016/j.bmc.2010.08.017
  • Primary Citation of Related Structures:  
    3VHE

  • PubMed Abstract: 
  • We synthesized a series of pyrrolo[3,2-d]pyrimidine derivatives and evaluated their application as type-II inhibitors of vascular endothelial growth factor receptor 2 (VEGFR2) kinase. Incorporation of a diphenylurea moiety at the C4-position of the p ...

    We synthesized a series of pyrrolo[3,2-d]pyrimidine derivatives and evaluated their application as type-II inhibitors of vascular endothelial growth factor receptor 2 (VEGFR2) kinase. Incorporation of a diphenylurea moiety at the C4-position of the pyrrolo[3,2-d]pyrimidine core via an oxygen linker resulted in compounds that were potent inhibitors of VEGFR2 kinase. Of these derivatives, compound 20d showed the strongest inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells (HUVEC). The co-crystal structure of 20d and VEGFR2 revealed that 20d binds to the inactive form of VEGFR2. Further studies indicated that 20d inhibited VEGFR2 kinase with slow dissociation kinetics and also inhibited PDGFR and Tie-2 kinases. Oral administration of the hydrochloride salt of 20d at 3mg/kg/day showed potent inhibition of tumor growth in a DU145 human prostate cancer cell xenograft nude mouse model.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd, 10, Wadai, Tsukuba, Ibaraki 300-4293, Japan. Ooguro_Yuuya@takeda.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2A359Homo sapiensMutation(s): 0 
Gene Names: FLK1KDRVEGFR2
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42Q
Query on 42Q

Download CCD File 
A
1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea
C21 H15 F4 N5 O2
TWOLOZGQZKJZKJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
42QKi:  23   nM  BindingDB
42QKi:  0.019999999552965164   nM  BindingDB
42QKi:  0.03999999910593033   nM  BindingDB
42QIC50:  0.029999999329447746   nM  BindingDB
42QIC50:  14   nM  BindingDB
42QIC50:  4.699999809265137   nM  BindingDB
42QIC50 :  6.199999809265137   nM  PDBBind
42QKd:  19   nM  BindingDB
42QIC50:  6.199999809265137   nM  Binding MOAD
42QKi:  4.599999904632568   nM  BindingDB
42QIC50:  6.199999809265137   nM  BindingDB
42QIC50:  46   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.34α = 90
b = 56.27β = 95.24
c = 52.07γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release