8PQJ

PDGFRA wild-type kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA.

Teuber, A.Schulz, T.Fletcher, B.S.Gontla, R.Muhlenberg, T.Zischinsky, M.L.Niggenaber, J.Weisner, J.Kleinbolting, S.B.Lategahn, J.Sievers, S.Muller, M.P.Bauer, S.Rauh, D.

(2024) Nat Commun 15: 63-63

  • DOI: https://doi.org/10.1038/s41467-023-44376-8
  • Primary Citation of Related Structures:  
    8PQ9, 8PQA, 8PQB, 8PQC, 8PQD, 8PQE, 8PQF, 8PQG, 8PQH, 8PQI, 8PQJ, 8PQK

  • PubMed Abstract: 

    Avapritinib is the only potent and selective inhibitor approved for the treatment of D842V-mutant gastrointestinal stromal tumors (GIST), the most common primary mutation of the platelet-derived growth factor receptor α (PDGFRA). The approval was based on the NAVIGATOR trial, which revealed overall response rates of more than 90%. Despite this transformational activity, patients eventually progress, mostly due to acquired resistance mutations or following discontinuation due to neuro-cognitive side effects. These patients have no therapeutic alternative and face a dismal prognosis. Notable, little is known about this drug's binding mode and its medicinal chemistry development, which is instrumental for the development of the next generation of drugs. Against this background, we solve the crystal structures of avapritinib in complex with wild-type and mutant PDGFRA and stem cell factor receptor (KIT), which provide evidence and understanding of inhibitor binding and lead to the identification of a sub-pocket (Gα-pocket). We utilize this information to design, synthesize and characterize avapritinib derivatives for the determination of key pharmacophoric features to overcome drug resistance and limit potential blood-brain barrier penetration.


  • 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, 44227, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-derived growth factor receptor alpha352Homo sapiensMutation(s): 0 
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
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.38α = 90
b = 49.18β = 100.78
c = 77.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean UnionEFRE-800400
German Federal Ministry for Education and ResearchGermany01ZX2201B
Other privateEx-2021-0033
Other governmentNW21-062C

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Database references
  • Version 1.3: 2024-08-07
    Changes: Database references