9GZH | pdb_00009gzh

PDGFRA-T674I in complex with covalent ponatinib derivative 19

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 

  • Deposited: 2024-10-04 Released: 2025-02-12 
  • Deposition Author(s): Teuber, A., Rauh, D., Mueller, M.P.
  • Funding Organization(s): German Research Foundation (DFG), European Regional Development Fund, German Federal Ministry for Education and Research, Other government, Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, and SAR of Covalent KIT and PDGFRA Inhibitors─Exploring Their Potential in Targeting GIST.

Schulz, T.Gontla, R.Teuber, A.Beerbaum, M.Fletcher, B.S.Muhlenberg, T.Kaitsiotou, H.Hardick, J.Jeyakumar, K.Keul, M.Muller, M.P.Sievers, S.Bauer, S.Rauh, D.

(2025) J Med Chem 68: 3238-3259

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02472
  • Primary Citation of Related Structures:  
    9GZH

  • PubMed Abstract: 

    Gastrointestinal stromal tumors (GIST), driven by KIT and PDGFRA mutations, are the most common mesenchymal tumors of the gastrointestinal tract. Although tyrosine kinase inhibitors (TKIs) have advanced treatment, resistance mutations and off-target toxicity limit their efficacy. This study develops covalent TKIs targeting drug-resistant GIST through structure-based design, synthesis, and biological evaluation. SAR studies provided key insights into mutant KIT and PDGFRA interactions, and the first crystal structure of PDGFRA bound to a covalent inhibitor is reported. These findings highlight the promise of covalent inhibitors for overcoming resistance and advancing safer, more effective therapies for advanced GIST.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, Dortmund 44227, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-derived growth factor receptor alpha355Homo sapiensMutation(s): 1 
Gene Names: PDGFRAPDGFR2RHEPDGFRA
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P16234 (Homo sapiens)
Explore P16234 
Go to UniProtKB:  P16234
PHAROS:  P16234
GTEx:  ENSG00000134853 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16234
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IRC (Subject of Investigation/LOI)
Query on A1IRC

Download Ideal Coordinates CCD File 
B [auth A]3-(2-imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-~{N}-[4-(propanoylamino)-3-(trifluoromethyl)phenyl]benzamide
C26 H20 F3 N5 O2
FTNOFDRVSQZWOA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.92α = 90
b = 135.92β = 90
c = 34.69γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRA 1055/3-2
European Regional Development FundEuropean UnionEFRE-800400
German Federal Ministry for Education and ResearchGermany01ZX2201B
Other governmentGermanyNW21-062C
Other privateEx-2021-0033

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references