Crystal structure of FGFR4 kinase domain with irreversible inhibitor 1

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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This is version 1.3 of the entry. See complete history


Development of a Potent and Specific FGFR4 Inhibitor for the Treatment of Hepatocellular Carcinoma.

Rezende Miranda, R.Fu, Y.Chen, X.Perino, J.Cao, P.Carpten, J.Chen, Y.Zhang, C.

(2020) J Med Chem 63: 11484-11497

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00044
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Abnormal activation of the fibroblast growth factor 19 (FGF19)/fibroblast growth factor receptor 4 (FGFR4) signaling pathway has been shown to drive the proliferation of a significant portion of hepatocellular carcinoma (HCC). Resistance and toxicity are serious drawbacks that have been observed upon use of the current first- and second-line treatment options for HCC, therefore warranting the investigation of alternative therapeutic approaches. We report the development and biological characterization of a covalent inhibitor that is highly potent and exquisitely specific to FGFR4. The crystal structure of this inhibitor in complex with FGFR4 was solved, confirming its covalent binding and revealing its binding mode. We also describe the first clickable probe for FGFR4 that can be used to directly measure target engagement in cells. Our compound exhibited great antitumor activity in HCC cell lines and tumor xenograft models. These results provide evidence of a promising therapeutic lead for the treatment of a subset of HCC patients.

  • Organizational Affiliation

    Department of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4311Homo sapiensMutation(s): 2 
Gene Names: FGFR4JTK2TKF
UniProt & NIH Common Fund Data Resources
Find proteins for P22455 (Homo sapiens)
Explore P22455 
Go to UniProtKB:  P22455
PHAROS:  P22455
GTEx:  ENSG00000160867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22455
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYU (Subject of Investigation/LOI)
Query on BYU

Download Ideal Coordinates CCD File 
B [auth A]N-[2-[[6-[2-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]amino]pyridin-3-yl]pyrimidin-4-yl]amino]-3-methyl-phenyl]prop-2-enamide
C27 H24 Cl2 N6 O3
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.502α = 90
b = 61.126β = 99.1
c = 61.412γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81570537

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2020-11-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description