8SWE

FGFR2 Kinase Domain Bound to Reversible Inhibitor Cmpd 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2.

Schonherr, H.Ayaz, P.Taylor, A.M.Casaletto, J.B.Toure, B.B.Moustakas, D.T.Hudson, B.M.Valverde, R.Zhao, S.O'Hearn, P.J.Foster, L.Sharon, D.A.Garfinkle, S.Giordanetto, F.Lescarbeau, A.Kurukulasuriya, R.Gerami-Moayed, N.Maglic, D.Bruderek, K.Naik, G.Gunaydin, H.Mader, M.M.Boezio, A.A.McLean, T.H.Chen, R.Wang, Y.Shaw, D.E.Watters, J.Bergstrom, D.A.

(2024) Proc Natl Acad Sci U S A 121: e2317756121-e2317756121

  • DOI: https://doi.org/10.1073/pnas.2317756121
  • Primary Citation of Related Structures:  
    8SWE, 8U1F

  • PubMed Abstract: 

    Fibroblast growth factor receptor (FGFR) kinase inhibitors have been shown to be effective in the treatment of intrahepatic cholangiocarcinoma and other advanced solid tumors harboring FGFR2 alterations, but the toxicity of these drugs frequently leads to dose reduction or interruption of treatment such that maximum efficacy cannot be achieved. The most common adverse effects are hyperphosphatemia caused by FGFR1 inhibition and diarrhea due to FGFR4 inhibition, as current therapies are not selective among the FGFRs. Designing selective inhibitors has proved difficult with conventional approaches because the orthosteric sites of FGFR family members are observed to be highly similar in X-ray structures. In this study, aided by analysis of protein dynamics, we designed a selective, covalent FGFR2 inhibitor. In a key initial step, analysis of long-timescale molecular dynamics simulations of the FGFR1 and FGFR2 kinase domains allowed us to identify differential motion in their P-loops, which are located adjacent to the orthosteric site. Using this insight, we were able to design orthosteric binders that selectively and covalently engage the P-loop of FGFR2. Our drug discovery efforts culminated in the development of lirafugratinib (RLY-4008), a covalent inhibitor of FGFR2 that shows substantial selectivity over FGFR1 (~250-fold) and FGFR4 (~5,000-fold) in vitro, causes tumor regression in multiple FGFR2 -altered human xenograft models, and was recently demonstrated to be efficacious in the clinic at doses that do not induce clinically significant hyperphosphatemia or diarrhea.


  • Organizational Affiliation

    Relay Therapeutics, Cambridge, MA 02139.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 2
A, B
316Homo sapiensMutation(s): 0 
Gene Names: FGFR2BEKKGFRKSAM
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens)
Explore P21802 
Go to UniProtKB:  P21802
GTEx:  ENSG00000066468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21802
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WXQ (Subject of Investigation/LOI)
Query on WXQ

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
N-{4-[4-amino-5-(4-methoxyphenyl)-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-6-yl]phenyl}prop-2-enamide
C23 H21 N5 O2
PVEZIQYTTJVILM-UHFFFAOYSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
D [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B],
G [auth B],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.46α = 90
b = 117.13β = 90
c = 64.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release