9BR4 | pdb_00009br4

Crystal structure of p53 Y220C mutant in complex with PC-9859


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9BR4

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Rezatapopt (PC14586), a First-in-Class, Small-Molecule Reactivator of p53 Y220C Mutant in Development.

Vu, B.T.Dominique, R.Fahr, B.J.Li, H.H.Fry, D.C.Xu, L.Yang, H.Puzio-Kuter, A.Good, A.Liu, B.Huang, K.S.Tanaka, N.Davis, T.W.Dumble, M.L.

(2025) ACS Med Chem Lett 16: 34-39

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00379
  • Primary Citation Related Structures: 
    9BR4

  • PubMed Abstract: 

    p53 is a potent transcription factor that is crucial in regulating cellular responses to stress. Mutations in the TP53 gene are found in >50% of human cancers, predominantly occurring in the DNA-binding domain (amino acids 94-292). The Y220C mutation accounts for 1.8% of all of the TP53 mutations and produces a thermally unstable protein. Rezatapopt (also known as PC14586) is the first small-molecule p53 Y220C reactivator being evaluated in clinical trials. Rezatapopt was specifically designed to tightly bind to a pocket created by the TP53 Y220C mutation. By stabilization of the p53 protein structure, rezatapopt restores p53 tumor suppressor functions. In mouse models with established human tumor xenografts harboring the TP53 Y220C mutation, rezatapopt demonstrated tumor inhibition and regression at well-tolerated doses. In Phase 1 clinical trials, rezatapopt demonstrated a favorable safety profile within the efficacious dose range and showed single-agent efficacy in heavily pretreated patients with various TP53 Y220C mutant solid tumors.


  • Organizational Affiliation
    • Discovery Chemistry, PMV Pharmaceuticals, Inc., 400 Alexander Park Drive, Suite 301, Princeton, New Jersey 08540, United States.

Macromolecule Content 

  • Total Structure Weight: 50.57 kDa 
  • Atom Count: 3,713 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 442 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ARZ
(Subject of Investigation/LOI)

Query on A1ARZ



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
2-methyl-2-{5-[(3-{4-[(1-methylpiperidin-4-yl)amino]-1-(2,2,2-trifluoroethyl)-1H-indol-2-yl}prop-2-yn-1-yl)amino]pyridin-2-yl}propanenitrile
C28 H31 F3 N6
ZEIVMOHWKJFVMK-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.72α = 90
b = 70.98β = 90
c = 104.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references