6V9C

Crystal structure of FGFR4 kinase domain in complex with covalent inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb6V9C/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-03-25 
• Deposition Author(s): Liu, J., Liu, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Discovery of Selective, Covalent FGFR4 Inhibitors with Antitumor Activity in Models of Hepatocellular Carcinoma.

Liu, H., Niu, D., Tham Sjin, R.T., Dubrovskiy, A., Zhu, Z., McDonald, J.J., Fahnoe, K., Wang, Z., Munson, M., Scholte, A., Barrague, M., Fitzgerald, M., Liu, J., Kothe, M., Sun, F., Murtie, J., Ge, J., Rocnik, J., Harvey, D., Ospina, B., Perron, K., Zheng, G., Shehu, E., D'Agostino, L.A.

(2020) ACS Med Chem Lett 11: 1899-1904

• PubMed: 33062171 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00601
• Primary Citation of Related Structures:  
  6V9C


• PubMed Abstract: 
  

Hepatocellular carcinoma (HCC) accounts for a majority of primary liver cancer and is one of the most common forms of cancer worldwide. Aberrant signaling of the FGF19-FGFR4 pathway leads to HCC in mice and is hypothesized to be a driver in FGF19 amplified HCC in humans. Multiple small molecule inhibitors have been pursued as targeted therapies for HCC in recent years, including several selective FGFR4 inhibitors that are currently being evaluated in clinical trials. Herein, we report a novel series of highly selective, covalent 2-amino-6,8-dimethyl-pyrido[2,3- d ]pyrimidin-7(8 H )-ones that potently and selectively inhibit FGFR4 signaling through covalent modification of Cys552, which was confirmed by X-ray crystallography. Correlative target occupancy and pFGFR4 inhibition were observed in vivo, as well as tumor regression in preclinical models of orthotopic and sorafenib-resistant HCC.

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Organizational Affiliation: 

Departments of Chemistry, Biology, and Biochemistry, Bristol Myers Squibb, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.58 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 279 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A	300	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QS7 (Subject of Investigation/LOI)	B [auth A]	N-[(3R,4S)-4-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}oxolan-3-yl]prop-2-enamide C23 H23 Cl2 N5 O5 ZIJVLVUPDVUSMA-UONOGXRCSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
QS7	BindingDB:  6V9C	IC50: min: 6.5, max: 500 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.067	α = 90
b = 58.67	β = 97.57
c = 60.747	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Liu, J., Liu, H.

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references