Crystal structure of minimal kinase domain of fibroblast growth factor receptor 1 in complex with 5-(2-thienyl)nicotinic acid

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors by structure-based virtual screening

Ravindranathan, K.P.Mandiyan, V.Ekkati, A.R.Bae, J.H.Schlessinger, J.Jorgensen, W.L.

(2010) J Med Chem 53: 1662-1672

  • DOI: https://doi.org/10.1021/jm901386e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Fibroblast growth factors (FGFs) play important roles in embryonic development, angiogenesis, wound healing, and cell proliferation and differentiation. In search of inhibitors of FGFR1 kinase, 2.2 million compounds were docked into the ATP binding site of the protein. A co-crystal structure, which shows two alternative conformations for the nucleotide binding loop, is reported. Docking was performed on both conformations and, ultimately, 23 diverse compounds were purchased and assayed. Following hit validation, two compounds 10 and 16, a benzylidene derivative of pseudothiohydantoin and a thienopyrimidinone derivative, respectively, were discovered that inhibit FGFR1 kinase with IC(50) values of 23 and 50 microM. Initial optimization of 16 led to the more unsaturated 40, which has significantly enhanced potency, 1.9 microM. The core structures represent new structural motifs for FGFR1 kinase inhibitors. The study also illustrates complexities associated with the choice of protein structures for docking, possible use of multiple kinase structures to seek selectivity, and hit identification.

  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic fibroblast growth factor receptor 1
A, B
317Homo sapiensMutation(s): 2 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.799α = 90
b = 58.304β = 107.36
c = 66.248γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-02-01
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description