4QQ5

Crystal Structure of FGF Receptor (FGFR) 4 Kinase Harboring the V550L Gate-Keeper Mutation in Complex With FIIN-2, an Irreversible Tyrosine Kinase Inhibitor Capable of Overcoming FGFR Kinase Gate-Keeper Mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.203 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DFG-out Mode of Inhibition by an Irreversible Type-1 Inhibitor Capable of Overcoming Gate-Keeper Mutations in FGF Receptors.

Huang, Z.Tan, L.Wang, H.Liu, Y.Blais, S.Deng, J.Neubert, T.A.Gray, N.S.Li, X.Mohammadi, M.

(2015) Acs Chem.Biol. 10: 299-309

  • DOI: 10.1021/cb500674s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drug-resistance acquisition through kinase gate-keeper mutations is a major hurdle in the clinic. Here, we determined the first crystal structures of the human FGFR4 kinase domain (FGFR4K) alone and complexed with ponatinib, a promiscuous type-2 (DFG ...

    Drug-resistance acquisition through kinase gate-keeper mutations is a major hurdle in the clinic. Here, we determined the first crystal structures of the human FGFR4 kinase domain (FGFR4K) alone and complexed with ponatinib, a promiscuous type-2 (DFG-out) kinase inhibitor, and an oncogenic FGFR4K harboring the V550L gate-keeper mutation bound to FIIN-2, a new type-1 irreversible inhibitor. Remarkably, like ponatinib, FIIN-2 also binds in the DFG-out mode despite lacking a functional group necessary to occupy the pocket vacated upon the DFG-out flip. Structural analysis reveals that the covalent bond between FIIN-2 and a cysteine, uniquely present in the glycine-rich loop of FGFR kinases, facilitates the DFG-out conformation, which together with the internal flexibility of FIIN-2 enables FIIN-2 to avoid the steric clash with the gate-keeper mutation that causes the ponatinib resistance. The structural data provide a blueprint for the development of next generation anticancer inhibitors through combining the salient inhibitory mechanisms of ponatinib and FIIN-2.


    Organizational Affiliation

    School of Pharmacy, Wenzhou Medical University , Wenzhou, Zhejiang 325035, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibroblast growth factor receptor 4
A
323Homo sapiensMutation(s): 2 
Gene Names: FGFR4 (JTK2, TKF)
EC: 2.7.10.1
Find proteins for P22455 (Homo sapiens)
Go to Gene View: FGFR4
Go to UniProtKB:  P22455
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
37O
Query on 37O

Download SDF File 
Download CCD File 
A
N-(4-{[3-(3,5-dimethoxyphenyl)-7-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]methyl}phenyl)propanamide
C35 H40 N8 O4
DKHGWJNITASDGF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.203 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 139.599α = 90.00
b = 139.599β = 90.00
c = 49.660γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references