The crystal structure of FGFR4 kinase domain in complex with N-(5-cyano-4-((2-methoxyethyl)amino)pyridin-2-yl)-7-(2,2,2-trifluoroacetyl)-3,4-dihydro-1,8-naphthyridine-1(2H)-carboxamide

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.212 

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This is version 2.2 of the entry. See complete history


Characterization of an aromatic trifluoromethyl ketone as a new warhead for covalently reversible kinase inhibitor design.

Zhang, Z.Wang, Y.Chen, X.Song, X.Tu, Z.Chen, Y.Zhang, Z.Ding, K.

(2021) Bioorg Med Chem 50: 116457-116457

  • DOI: https://doi.org/10.1016/j.bmc.2021.116457
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An aromatic trifluoromethyl ketone moiety was characterized as a new warhead for covalently reversible kinase inhibitor design to target the non-catalytic cysteine residue. Potent and selective covalently reversible inhibitors of FGFR4 kinase were successfully designed and synthesized by utilizing this new warhead. The binding mode of a representative inhibitor was fully characterized by using multiple technologies including MALDI-TOF mass spectrometry, dialysis assay and X-ray crystallographic studies etc. This functional group was also successfully applied to discovery of a new JAK3 inhibitor, suggesting its potential application in designing other kinase inhibitors.

  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4
A, B
301Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7IF (Subject of Investigation/LOI)
Query on 7IF

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H23 F3 N6 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.37α = 90
b = 66.785β = 90
c = 184.174γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 2.0: 2022-05-04
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2022-09-07
    Changes: Database references
  • Version 2.2: 2023-11-29
    Changes: Data collection, Refinement description