6GGF

Structure of the p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9328


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structure-guided molecular chaperone approach for restoring the transcriptional activity of the p53 cancer mutant Y220C.

Bauer, M.R.Jones, R.N.Tareque, R.K.Springett, B.Dingler, F.A.Verduci, L.Patel, K.J.Fersht, A.R.Joerger, A.C.Spencer, J.

(2019) Future Med Chem 11: 2491-2504

  • DOI: 10.4155/fmc-2019-0181
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <b>Aim: </b> The p53 cancer mutation Y220C creates a conformationally unstable protein with a unique elongated surface crevice that can be targeted by molecular chaperones. We report the structure-guided optimization of the carbazole-based stabilize ...

    Aim: The p53 cancer mutation Y220C creates a conformationally unstable protein with a unique elongated surface crevice that can be targeted by molecular chaperones. We report the structure-guided optimization of the carbazole-based stabilizer PK083. Materials & methods:  Biophysical, cellular and x-ray crystallographic techniques have been employed to elucidate the mode of action of the carbazole scaffolds.  Results: Targeting an unoccupied subsite of the surface crevice with heterocycle-substituted PK083 analogs resulted in a 70-fold affinity increase to single-digit micromolar levels, increased thermal stability and decreased rate of aggregation of the mutant protein. PK9318, one of the most potent binders, restored p53 signaling in the liver cancer cell line HUH-7 with homozygous Y220C mutation. Conclusion: The p53-Y220C mutant is an excellent paradigm for the development of mutant p53 rescue drugs via protein stabilization. Similar rescue strategies may be applicable to other cavity-creating p53 cancer mutations.


    Related Citations: 
    • Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.
      Joerger, A.C.,Ang, H.C.,Fersht, A.R.
      (2006) Proc. Natl. Acad. Sci. U.S.A. 103: 15056


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.,Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.,Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QJ, UK.,Buchmann Institute for Molecular Life Sciences & Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular tumor antigen p53
A, B
219Homo sapiensMutation(s): 5 
Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens)
Go to Gene View: TP53
Go to UniProtKB:  P04637
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EXQ
Query on EXQ

Download SDF File 
Download CCD File 
A, B
[9-ethyl-7-(4-methylthiophen-2-yl)carbazol-3-yl]methyl-methyl-azanium
C21 H23 N2 S
JGJSOWKZKLYSTB-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.110α = 90.00
b = 71.209β = 90.00
c = 105.351γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyJO 1473/1-1

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references