8KH8

Crystal structure of FGFR4(V550L) kinase domain with 8z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of 6-Formylpyridyl Urea Derivatives as Potent Reversible-Covalent Fibroblast Growth Factor Receptor 4 Inhibitors with Improved Anti-Hepatocellular Carcinoma Activity.

Yang, F.Lin, Q.Song, X.Huang, H.Chen, X.Tan, J.Li, Y.Zhou, Y.Tu, Z.Du, H.Zhang, Z.M.Ortega, R.Lin, X.Patterson, A.V.Smaill, J.B.Chen, Y.Lu, X.

(2024) J Med Chem 67: 2667-2689

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01810
  • Primary Citation of Related Structures:  
    8KH6, 8KH7, 8KH8, 8KH9, 8W5C

  • PubMed Abstract: 

    Fibroblast growth factor receptor 4 (FGFR4) has been considered as a potential anticancer target due to FGF19/FGFR4 mediated aberrant signaling in hepatocellular carcinoma (HCC). Several FGFR4 inhibitors have been reported, but none have gained approval. Herein, a series of 5-formyl-pyrrolo[3,2- b ]pyridine-3-carboxamides and a series of 6-formylpyridyl ureas were characterized as selective reversible-covalent FGFR4 inhibitors. The representative 6-formylpyridyl urea 8z exhibited excellent potency against FGFR4 WT , FGFR4 V550L , and FGFR4 V550M with IC 50 values of 16.3, 12.6, and 57.3 nM, respectively. It also potently suppressed proliferation of Ba/F3 cells driven by FGFR4 WT , FGFR4 V550L , and FGFR4 V550M , and FGFR4-dependent Hep3B and Huh7 HCC cells, with IC 50 values of 1.2, 13.5, 64.5, 15.0, and 20.4 nM, respectively. Furthermore, 8z displayed desirable microsomal stability and significant in vivo efficacy in the Huh7 HCC cancer xenograft model in nude mice. The study provides a promising new lead for anticancer drug discovery directed toward overcoming FGFR4 gatekeeper mutation mediated resistance in HCC patients.


  • Organizational Affiliation

    State Key Laboratory of Bioactive Molecules and Druggability Assessment, 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.


Macromolecules
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
EC: 2.7.10.1
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VVW (Subject of Investigation/LOI)
Query on VVW

Download Ideal Coordinates CCD File 
C [auth A]1-[4-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-5-cyano-pyridin-2-yl]-3-[6-methanoyl-5-[(4-methyl-2-oxidanylidene-piperazin-1-yl)methyl]-3-(2-morpholin-4-ylethoxy)pyridin-2-yl]urea
C32 H35 Cl2 N9 O6
AEFSLXKVONEDJJ-HXUWFJFHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.141α = 90
b = 61.457β = 97.82
c = 60.417γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary