Crystal structure of FGFR4 kinase domain in complex with compound 5

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design.

Wang, Y.Dai, Y.Wu, X.Li, F.Liu, B.Li, C.Liu, Q.Zhou, Y.Wang, B.Zhu, M.Cui, R.Tan, X.Xiong, Z.Liu, J.Tan, M.Xu, Y.Geng, M.Jiang, H.Liu, H.Ai, J.Zheng, M.

(2019) J Med Chem 62: 7473-7488

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00510
  • Primary Citation of Related Structures:  
    6ITJ, 6IUO, 6IUP

  • PubMed Abstract: 

    Alterations of fibroblast growth factor receptors (FGFRs) play key roles in numerous cancer progression and development, which makes FGFRs attractive targets in the cancer therapy. In the present study, based on a newly devised FGFR target-specific scoring function, a novel FGFR inhibitor hit was identified through virtual screening. Hit-to-lead optimization was then performed by integrating molecular docking and site-of-metabolism predictions with an array of in vitro evaluations and X-ray cocrystal structure determination, leading to a covalent FGFR inhibitor 15 , which showed a highly selective and potent FGFR inhibition profile. Pharmacokinetic assessment, protein kinase profiling, and hERG inhibition evaluation were also conducted, and they confirmed the value of 15 as a lead for further investigation. Overall, this study exemplifies the importance of the integrative use of computational methods and experimental techniques in drug discovery.

  • Organizational Affiliation

    School of Chemistry , Shanghai University , 99 ShangDa Road , Shanghai 200444 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4322Homo sapiensMutation(s): 1 
Gene Names: FGFR4
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
AX0 (Subject of Investigation/LOI)
Query on AX0

Download Ideal Coordinates CCD File 
B [auth A]N-{4-[4-amino-3-(3,5-dimethyl-1-benzofuran-2-yl)-7-oxo-6,7-dihydro-2H-pyrazolo[3,4-d]pyridazin-2-yl]phenyl}prop-2-enamide
C24 H20 N6 O3
DMS (Subject of Investigation/LOI)
Query on DMS

Download Ideal Coordinates CCD File 
C2 H6 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.4α = 90
b = 61.15β = 99.22
c = 61.4γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2019-11-06 
  • Deposition Author(s): Xu, Y., Liu, Q.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description