9BR3 | pdb_00009br3

Crystal structure of p53 Y220C mutant in complex with PC-10709


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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Literature

Restoration of the Tumor Suppressor Function of Y220C-Mutant p53 by Rezatapopt, a Small-Molecule Reactivator.

Puzio-Kuter, A.M.Xu, L.McBrayer, M.K.Dominique, R.Li, H.H.Fahr, B.J.Brown, A.M.Wiebesiek, A.E.Russo, B.M.Mulligan, C.L.Yang, H.Battaglia, J.Robell, K.A.Thomas, D.H.Huang, K.S.Solovyov, A.Greenbaum, B.D.Oliner, J.D.Davis, T.W.Dumble, M.L.Johnson, M.L.Xiong, S.Yang, P.Lozano, G.Fellous, M.M.Vu, B.T.Schram, A.M.Levine, A.J.Poyurovsky, M.V.

(2025) Cancer Discov 15: 1159-1179

  • DOI: https://doi.org/10.1158/2159-8290.CD-24-1421
  • Primary Citation of Related Structures:  
    9BR3

  • PubMed Abstract: 

    Restoration of the tumor suppressor function of tumor-associated p53 mutants, including the Y220C substitution, has posed a significant challenge for therapeutic discovery. Here, we describe rezatapopt (PC14586), part of a series of compounds designed to reactivate the p53 Y220C mutant. These compounds restore p53 tumor suppressor function by correcting its conformation and enabling it to bind DNA and activate downstream target genes, thus inducing anti-proliferative changes in tumor cells. Our findings are supported by biochemical and structural analysis, in vitro and in vivo transcriptomics, and functional data, revealing the recovery of multiple aspects of the wild type p53 program. These compounds demonstrate potent anti-tumor activity in preclinical models as single agents and in combination with immunotherapy. Currently, rezatapopt is being evaluated in a registrational Phase 2 clinical trial for patients with advanced solid tumors harboring the TP53 Y220C mutation.


  • Organizational Affiliation
    • PMV Pharmaceuticals, Inc, Princeton, New Jersey, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53
A, B
221Homo sapiensMutation(s): 4 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.96α = 90
b = 71.21β = 90
c = 104.85γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Database references