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 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1)
A, B
310Homo sapiensMutation(s): 3 
EC: 2.7.1.112
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
PHAROS:  P11362
GTEx:  ENSG00000077782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11362
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PD1
Query on PD1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
PD1 PDBBind:  2FGI Ki: 45.2 (nM) from 1 assay(s)
Binding MOAD:  2FGI Ki: 36.4 (nM) from 1 assay(s)
BindingDB:  2FGI IC50: min: 5, max: 30 (nM) from 4 assay(s)
EC50: 21 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection