9K0I | pdb_00009k0i

Crystal structure of FGFR4 kinase domain with 32a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9K0I

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of Aminoindazole derivatives as highly selective covalent inhibitors for wild-type and mutant FGFR4.

Guo, J.Chen, X.Li, X.Wang, X.Shao, M.Song, X.Zhang, L.Huang, S.Patterson, A.V.Smaill, J.B.Zhou, Y.Yu, X.Chen, Y.Lu, X.

(2025) Bioorg Chem 160: 108469-108469

  • DOI: https://doi.org/10.1016/j.bioorg.2025.108469
  • Primary Citation Related Structures: 
    9K0I, 9K0J

  • PubMed Abstract: 

    The Fibroblast growth factor receptor 4 (FGFR4) has emerged as a potential oncogenic driver in hepatocellular carcinoma (HCC), primarily due to aberrations in the FGFR4-FGF19 signaling axis. Although the FGFR4-selective inhibitors have been reported, none have received approval. Further, the clinical acquired resistance caused by FGFR4 mutations has become an unmet clinical need for cancer therapy. In this study, we designed and synthesized a series of 3-amido-1H-indazole-based FGFR4 irreversible inhibitors, targeting both wild-type FGFR4 and the gatekeeper and molecular brake mutants. The representative compound, 48c, exhibited potent inhibitory activity against FGFR4 WT kinase (IC 50  = 2.9 nM) and picomolar activity against FGFR4 WT , FGFR4 V550L , and FGFR4 V550M -driven Ba/F3 cell lines (IC 50  < 0.1, 0.3, and 0.3 nM, respectively). 48c exhibited high selectivity across a panel of 66 kinases harboring a cysteine at the hinge region, highlighting its potential as a promising therapeutic candidate for overcoming resistance in FGFR4-associated tumors.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China.

Macromolecule Content 

  • Total Structure Weight: 36.06 kDa 
  • Atom Count: 2,588 
  • Modeled Residue Count: 300 
  • Deposited Residue Count: 311 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4311Homo 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
GTEx:  ENSG00000160867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22455
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EEW
(Subject of Investigation/LOI)

Query on A1EEW



Download:Ideal Coordinates CCD File
B [auth A](2~{S})-~{N}-[2-[[5-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1~{H}-indazol-3-yl]amino]-3-fluoranyl-5-(4-morpholin-4-ylpiperidin-1-yl)phenyl]-2-cyano-3-cyclopropyl-propanamide
C36 H39 Cl2 F N8 O3
CRSNSQWEEMLLEQ-GGAORHGYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.174α = 90
b = 61.875β = 97.83
c = 59.868γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81974074
National Natural Science Foundation of China (NSFC)China82172654
National Natural Science Foundation of China (NSFC)China82202920

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Database references