Crystal structure of FGFR4(V550L) kinase domain with 7v

Experimental Data Snapshot

  • Resolution: 2.32 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design, Synthesis, and Biological Evaluation of Aminoindazole Derivatives as Highly Selective Covalent Inhibitors of Wild-Type and Gatekeeper Mutant FGFR4.

Shao, M.Chen, X.Yang, F.Song, X.Zhou, Y.Lin, Q.Fu, Y.Ortega, R.Lin, X.Tu, Z.Patterson, A.V.Smaill, J.B.Chen, Y.Lu, X.

(2022) J Med Chem 65: 5113-5133

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00096
  • Primary Citation of Related Structures:  
    7WCT, 7WCW, 7WCX

  • PubMed Abstract: 

    Aberrant FGF19/FGFR4 signaling has been shown to be an oncogenic driver of growth and survival in human hepatocellular carcinoma (HCC) with several pan-FGFR inhibitors and FGFR4-selective inhibitors currently being evaluated in the clinic. However, FGFR4 gatekeeper mutation induced acquired resistance remains an unmet clinical challenge for HCC treatment. Thus, a series of aminoindazole derivatives were designed and synthesized as new irreversible inhibitors of wild-type and gatekeeper mutant FGFR4. One representative compound ( 7v ) exhibited excellent potency against FGFR4, FGFR4 V550L , and FGFR4 V550M with nanomolar activity in both the biochemical and cellular assays while sparing FGFR1/2/3. While compound 7v demonstrated modest in vivo antitumor efficacy in nude mice bearing the Huh-7 xenograft model consistent with its unfavorable pharmacokinetic properties, it provides a promising new starting point for future drug discovery combating FGFR4 gatekeeper mediated resistance in HCC patients.

  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4309Homo sapiensMutation(s): 3 
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
90F (Subject of Investigation/LOI)
Query on 90F

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[2-[[5-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1~{H}-indazol-3-yl]amino]-3-fluoranyl-5-(4-morpholin-4-ylpiperidin-1-yl)phenyl]propanamide
C32 H36 Cl2 F N7 O3
Query on SO4

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

Experimental Data

  • Resolution: 2.32 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.984α = 90
b = 61.353β = 97.61
c = 60.531γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81570537
National Natural Science Foundation of China (NSFC)China81974074
National Natural Science Foundation of China (NSFC)China82172654

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description