6JPE | pdb_00006jpe

Crystal structure of FGFR4 kinase domain with irreversible inhibitor 1

• PDB DOI: https://doi.org/10.2210/pdb6JPE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-03-26 Released: 2020-05-06 
• Deposition Author(s): Chen, X., Dai, S., Zhou, Z., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.183 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Development of a Potent and Specific FGFR4 Inhibitor for the Treatment of Hepatocellular Carcinoma.

Rezende Miranda, R., Fu, Y., Chen, X., Perino, J., Cao, P., Carpten, J., Chen, Y., Zhang, C.

(2020) J Med Chem 63: 11484-11497

• PubMed: 33030342 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00044
• Primary Citation Related Structures: 
  6JPE


• PubMed Abstract: 
  

  Abnormal activation of the fibroblast growth factor 19 (FGF19)/fibroblast growth factor receptor 4 (FGFR4) signaling pathway has been shown to drive the proliferation of a significant portion of hepatocellular carcinoma (HCC). Resistance and toxicity are serious drawbacks that have been observed upon use of the current first- and second-line treatment options for HCC, therefore warranting the investigation of alternative therapeutic approaches. We report the development and biological characterization of a covalent inhibitor that is highly potent and exquisitely specific to FGFR4. The crystal structure of this inhibitor in complex with FGFR4 was solved, confirming its covalent binding and revealing its binding mode. We also describe the first clickable probe for FGFR4 that can be used to directly measure target engagement in cells. Our compound exhibited great antitumor activity in HCC cell lines and tumor xenograft models. These results provide evidence of a promising therapeutic lead for the treatment of a subset of HCC patients.

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Organizational Affiliation: 
• Department of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States.
Department of Oncology, NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Central South University, Changsha, Hunan 410008, China.
Key Laboratory of Medical Genetics and College of Life Science, Central South University, Changsha, Hunan 410008, China.
BridGene Biosciences Inc., 1230 Bordeaux Dr, Sunnyvale, California 94089, United States.
USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States.
National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.41 kDa 
• Atom Count: 2,858 
• Modeled Residue Count: 298 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A	311	Homo sapiens	Mutation(s): 2  Gene Names: FGFR4, JTK2, TKF 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BYU (Subject of Investigation/LOI)	B [auth A]	N-[2-[[6-[2-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]amino]pyridin-3-yl]pyrimidin-4-yl]amino]-3-methyl-phenyl]prop-2-enamide C27 H24 Cl2 N6 O3 ZQYUWUUBHKOFPC-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.183 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.502	α = 90
b = 61.126	β = 99.1
c = 61.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Chen, X., Dai, S., Zhou, Z., Chen, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81570537

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Database references
• Version 1.2: 2020-11-04
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary