The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

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Discovery of KIN-3248, An Irreversible, Next Generation FGFR Inhibitor for the Treatment of Advanced Tumors Harboring FGFR2 and/or FGFR3 Gene Alterations.

Tyhonas, J.S.Arnold, L.D.Cox, J.M.Franovic, A.Gardiner, E.Grandinetti, K.Kania, R.Kanouni, T.Lardy, M.Li, C.Martin, E.S.Miller, N.Mohan, A.Murphy, E.A.Perez, M.Soroceanu, L.Timple, N.Uryu, S.Womble, S.Kaldor, S.W.

(2024) J Med Chem 67: 1734-1746

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01819
  • Primary Citation of Related Structures:  
    8UDT, 8UDU, 8UDV

  • PubMed Abstract: 

    Fibroblast growth factor receptor (FGFR) alterations are present as oncogenic drivers and bypass mechanisms in many forms of cancer. These alterations can include fusions, amplifications, rearrangements, and mutations. Acquired drug resistance to current FGFR inhibitors often results in disease progression and unfavorable outcomes for patients. Genomic profiling of tumors refractory to current FGFR inhibitors in the clinic has revealed several acquired driver alterations that could be the target of next generation therapeutics. Herein, we describe how structure-based drug design (SBDD) was used to enable the discovery of the potent and kinome selective pan-FGFR inhibitor KIN-3248 , which is active against many acquired resistance mutations. KIN-3248 is currently in phase I clinical development for the treatment of advanced tumors harboring FGFR2 and/or FGFR3 gene alterations.

  • Organizational Affiliation

    Kinnate Biopharma, San Diego, California 92130, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 3
A, B, C
297Homo sapiensMutation(s): 1 
Gene Names: FGFR3JTK4
UniProt & NIH Common Fund Data Resources
Find proteins for P22607 (Homo sapiens)
Explore P22607 
Go to UniProtKB:  P22607
GTEx:  ENSG00000068078 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22607
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WIQ (Subject of Investigation/LOI)
Query on WIQ

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C]
C26 H30 Cl N7 O3
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
M [auth C]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.664α = 90
b = 54.513β = 120.22
c = 128.718γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references