Crystal structure of FGFR4 kinase domain with 10t

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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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 5-Formyl-pyrrolo[3,2- b ]pyridine-3-carboxamides as New Selective, Potent, and Reversible-Covalent FGFR4 Inhibitors.

Yang, F.Chen, X.Song, X.Ortega, R.Lin, X.Deng, W.Guo, J.Tu, Z.Patterson, A.V.Smaill, J.B.Chen, Y.Lu, X.

(2022) J Med Chem 65: 14809-14831

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01319
  • Primary Citation of Related Structures:  
    7YBO, 7YBP, 7YBX, 7YC1, 7YC3

  • PubMed Abstract: 

    The FGF19-FGFR4 signaling pathway has been extensively studied as a promising target for the treatment of hepatocellular carcinoma (HCC). Several FGFR4-selective inhibitors have been developed, but none of them receives approval. Additionally, acquired resistance caused by FGFR4 gatekeeper mutations is emerging as a serious limitation for these targeted therapies. Herein, we report a novel series of 5-formyl-pyrrolo[3,2- b ]pyridine derivatives as new reversible-covalent inhibitors targeting wild-type and gatekeeper mutant variants of FGFR4 kinase. The representative compound 10z exhibited single-digit nanomolar activity against wild-type FGFR4 and the FGFR4 V550L/M mutant variants in biochemical and Ba/F3 cellular assays, while sparing FGFR1/2/3. Furthermore, 10z showed significant antiproliferative activity against Hep3B, JHH-7, and HuH-7 HCC cells with IC 50 values of 37, 32, and 94 nM, respectively. MALDI-TOF-MS and X-ray protein crystallography studies were consistent with 10z acting as a reversible-covalent inhibitor of FGFR4, serving as a promising lead compound for further anticancer drug development.

  • 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 4311Homo sapiensMutation(s): 1 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IIW (Subject of Investigation/LOI)
Query on IIW

Download Ideal Coordinates CCD File 
B [auth A]6-bromanyl-~{N}-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-5-methanoyl-1-(2-morpholin-4-ylethyl)pyrrolo[3,2-b]pyridine-3-carboxamide
C24 H26 Br N7 O4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.333α = 90
b = 61.038β = 98.01
c = 60.516γ = 90
Software Package:
Software NamePurpose
HKL-2000data 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: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description