2FGI

CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1 IN COMPLEX WITH INHIBITOR PD173074


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain.

Mohammadi, M.Froum, S.Hamby, J.M.Schroeder, M.C.Panek, R.L.Lu, G.H.Eliseenkova, A.V.Green, D.Schlessinger, J.Hubbard, S.R.

(1998) EMBO J 17: 5896-5904

  • DOI: 10.1093/emboj/17.20.5896
  • Primary Citation of Related Structures:  
    2FGI

  • PubMed Abstract: 
  • Angiogenesis, the sprouting of new blood vessels from pre-existing ones, is an essential physiological process in development, yet also plays a major role in the progression of human diseases such as diabetic retinopathy, atherosclerosis and cancer. ...

    Angiogenesis, the sprouting of new blood vessels from pre-existing ones, is an essential physiological process in development, yet also plays a major role in the progression of human diseases such as diabetic retinopathy, atherosclerosis and cancer. The effects of the most potent angiogenic factors, vascular endothelial growth factor (VEGF), angiopoietin and fibroblast growth factor (FGF) are mediated through cell surface receptors that possess intrinsic protein tyrosine kinase activity. In this report, we describe a synthetic compound of the pyrido[2,3-d]pyrimidine class, designated PD 173074, that selectively inhibits the tyrosine kinase activities of the FGF and VEGF receptors. We show that systemic administration of PD 173074 in mice can effectively block angiogenesis induced by either FGF or VEGF with no apparent toxicity. To elucidate the determinants of selectivity, we have determined the crystal structure of PD 173074 in complex with the tyrosine kinase domain of FGF receptor 1 at 2.5 A resolution. A high degree of surface complementarity between PD 173074 and the hydrophobic, ATP-binding pocket of FGF receptor 1 underlies the potency and selectivity of this inhibitor. PD 173074 is thus a promising candidate for a therapeutic angiogenesis inhibitor to be used in the treatment of cancer and other diseases whose progression is dependent upon new blood vessel formation.


    Organizational Affiliation

    Department of Pharmacology, New York University Medical Center, New York, NY 10016, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1)AB310Homo sapiensMutation(s): 3 
Gene Names: FGFR1BFGFRCEKFGFBRFLGFLT2HBGFR
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
NIH Common Fund Data Resources
PHAROS  P11362
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD1
Query on PD1

Download CCD File 
A, B
1-TERT-BUTYL-3-[6-(3,5-DIMETHOXY-PHENYL)-2-(4-DIETHYLAMINO-BUTYLAMINO)-PYRIDO[2,3-D]PYRIMIDIN-7-YL]-UREA
C28 H41 N7 O3
DXCUKNQANPLTEJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PD1IC50:  28   nM  BindingDB
PD1IC50:  30   nM  BindingDB
PD1IC50:  5   nM  BindingDB
PD1EC50:  21   nM  BindingDB
PD1Ki :  45.20000076293945   nM  PDBBind
PD1Ki:  36.400001525878906   nM  Binding MOAD
PD1IC50:  22   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.79α = 90
b = 57.38β = 107.55
c = 66.18γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance