Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 19

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Discovery of Aminopyrazole Derivatives as Potent Inhibitors of Wild-Type and Gatekeeper Mutant FGFR2 and 3.

Brawn, R.A.Cook, A.Omoto, K.Ke, J.Karr, C.Colombo, F.Virrankoski, M.Prajapati, S.Reynolds, D.Bolduc, D.M.Nguyen, T.V.Gee, P.Borrelli, D.Caleb, B.Yao, S.Irwin, S.Larsen, N.A.Selvaraj, A.Zhao, X.Ioannidis, S.

(2021) ACS Med Chem Lett 12: 93-98

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00517
  • Primary Citation of Related Structures:  
    7KIA, 7KIE

  • PubMed Abstract: 

    Fibroblast growth factor receptors (FGFR) 2 and 3 have been established as drivers of numerous types of cancer with multiple drugs approved or entering late stage clinical trials. A limitation of current inhibitors is vulnerability to gatekeeper resistance mutations. Using a combination of targeted high-throughput screening and structure-based drug design, we have developed a series of aminopyrazole based FGFR inhibitors that covalently target a cysteine residue on the P-loop of the kinase. The inhibitors show excellent activity against the wild-type and gatekeeper mutant versions of the enzymes. Further optimization using SAR analysis and structure-based drug design led to analogues with improved potency and drug metabolism and pharmacokinetics properties.

  • Organizational Affiliation

    H3 Biomedicine, 300 Technology Square, Cambridge, Massachusetts 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 2
A, B
308Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens)
Explore P21802 
Go to UniProtKB:  P21802
PHAROS:  P21802
GTEx:  ENSG00000066468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21802
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.98α = 90
b = 117.3β = 90
c = 63.81γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description