7EAX

Crystal complex of p53-V272M and antimony ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Repurposing antiparasitic antimonials to noncovalently rescue temperature-sensitive p53 mutations.

Tang, Y.Song, H.Wang, Z.Xiao, S.Xiang, X.Zhan, H.Wu, L.Wu, J.Xing, Y.Tan, Y.Liang, Y.Yan, N.Li, Y.Li, J.Wu, J.Zheng, D.Jia, Y.Chen, Z.Li, Y.Zhang, Q.Zhang, J.Zeng, H.Tao, W.Liu, F.Wu, Y.Lu, M.

(2022) Cell Rep 39: 110622-110622

  • DOI: https://doi.org/10.1016/j.celrep.2022.110622
  • Primary Citation of Related Structures:  
    7EAX

  • PubMed Abstract: 

    The tumor suppressor p53 is inactivated by over hundreds of heterogenous mutations in cancer. Here, we purposefully selected phenotypically reversible temperature-sensitive (TS) p53 mutations for pharmacological rescue with thermostability as the compound-screening readout. This rational screening identified antiparasitic drug potassium antimony tartrate (PAT) as an agent that can thermostabilize the representative TS mutant p53-V272M via noncovalent binding. PAT met the three basic criteria for a targeted drug: availability of a co-crystal structure, compatible structure-activity relationship, and intracellular target specificity, consequently exhibiting antitumor activity in a xenograft mouse model. At the antimony dose in clinical antiparasitic therapy, PAT effectively and specifically rescued p53-V272M in patient-derived primary leukemia cells in single-cell RNA sequencing. Further scanning of 815 frequent p53-missense mutations identified 65 potential PAT-treatable mutations, most of which were temperature sensitive. These results lay the groundwork for repurposing noncovalent antiparasitic antimonials for precisely treating cancers with the 65 p53 mutations.


  • Organizational Affiliation

    Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53
A, B, C, D
194Homo sapiensMutation(s): 1 
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: 2.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.876α = 90
b = 72.551β = 90
c = 85.067γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81622002
National Natural Science Foundation of China (NSFC)China81861130368
National Natural Science Foundation of China (NSFC)China82073292
Other governmentChinaShanghai Youth Talent Development Program (2017275)
Other governmentChinaShanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36)
Other governmentChinaShanghai Collaborative Innovation Center for Translational Medicine (TM201902)
Other governmentChinaFoundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description