6V9C

Crystal structure of FGFR4 kinase domain in complex with covalent inhibitor


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4A300Homo sapiensMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QS7
Query on QS7

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QS7IC50:  100   nM  BindingDB
QS7IC50:  500   nM  BindingDB
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 = 44.067α = 90
b = 58.67β = 97.57
c = 60.747γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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