8CG7 | pdb_00008cg7

Structure of p53 cancer mutant Y220C with arylation at Cys182 and Cys277


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Structure-Reactivity Studies of 2-Sulfonylpyrimidines Allow Selective Protein Arylation.

Pichon, M.M.Drelinkiewicz, D.Lozano, D.Moraru, R.Hayward, L.J.Jones, M.McCoy, M.A.Allstrum-Graves, S.Balourdas, D.I.Joerger, A.C.Whitby, R.J.Goldup, S.M.Wells, N.Langley, G.J.Herniman, J.M.Baud, M.G.J.

(2023) Bioconjug Chem 34: 1679-1687

  • DOI: https://doi.org/10.1021/acs.bioconjchem.3c00322
  • Primary Citation of Related Structures:  
    8CG7

  • PubMed Abstract: 

    Protein arylation has attracted much attention for developing new classes of bioconjugates with improved properties. Here, we have evaluated 2-sulfonylpyrimidines as covalent warheads for the mild, chemoselective, and metal free cysteine S -arylation. 2-Sulfonylpyrimidines react rapidly with cysteine, resulting in stable S -heteroarylated adducts at neutral pH. Fine tuning the heterocyclic core and exocyclic leaving group allowed predictable S N Ar reactivity in vitro , covering >9 orders of magnitude. Finally, we achieved fast chemo- and regiospecific arylation of a mutant p53 protein and confirmed arylation sites by protein X-ray crystallography. Hence, we report the first example of a protein site specifically S -arylated with iodo-aromatic motifs. Overall, this study provides the most comprehensive structure-reactivity relationship to date on heteroaryl sulfones and highlights 2-sulfonylpyrimidine as a synthetically tractable and protein compatible covalent motif for targeting reactive cysteines, expanding the arsenal of tunable warheads for modern covalent ligand discovery.


  • Organizational Affiliation

    School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53
A, B
219Homo sapiensMutation(s): 5 
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
A1IH3 (Subject of Investigation/LOI)
Query on A1IH3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
5-iodanyl-2-methylsulfonyl-pyrimidine
C5 H5 I N2 O2 S
HFGWJMJTMDNNIT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.881α = 90
b = 71.046β = 90
c = 104.887γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IH3Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyJO 1473/1-3

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 2.0: 2024-07-24
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Polymer sequence, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Structure summary