2X0U

STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO A 2-amino substituted benzothiazole scaffold

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Toward the Rational Design of P53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant.

Basse, N., Kaar, J.L., Settanni, G., Joerger, A.C., Rutherford, T.J., Fersht, A.R.

(2010) Chem.Biol. 17: 46

  • DOI: 10.1016/j.chembiol.2009.12.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The p53 cancer mutation Y220C induces formation of a cavity on the protein's surface that can accommodate stabilizing small molecules. We combined fragment screening and molecular dynamics to assess the druggability of p53-Y220C and map ligand intera ...

    The p53 cancer mutation Y220C induces formation of a cavity on the protein's surface that can accommodate stabilizing small molecules. We combined fragment screening and molecular dynamics to assess the druggability of p53-Y220C and map ligand interaction sites within the mutational cavity. Elucidation of the binding mode of fragment hits by crystallography yielded a clear picture of how a drug might dock in the cavity. Simulations that solvate the protein with isopropanol found additional sites that extend the druggable surface. Moreover, structural observations and simulation revealed the dynamic landscape of the cavity, which improves our understanding of the impact of the mutation on p53 stability. This underpins the importance of considering flexibility of the cavity in screening for optimized ligands. Our findings provide a blueprint for the design of effective drugs that rescue p53-Y220C.

    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.USA 103: 15056

    Organizational Affiliation: 

    Medical Research Council Centre for Protein Engineering, Cambridge, UK.




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 2 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
X0U
Query on X0U
Download SDF File 
Download CCD File 
B
6,7-DIHYDRO[1,4]DIOXINO[2,3-F][1,3]BENZOTHIAZOL-2-AMINE
C9 H8 N2 O2 S
IURPFIBKOPUBIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.060α = 90.00
b = 71.140β = 90.00
c = 105.410γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other