2VUK

Structure of the p53 core domain mutant Y220C bound to the stabilizing small-molecule drug PhiKan083


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeted Rescue of a Destabilized Mutant of P53 by an in Silico Screened Drug.

Boeckler, F.M.Joerger, A.C.Jaggi, G.Rutherford, T.J.Veprintsev, D.B.Fersht, A.R.

(2008) Proc.Natl.Acad.Sci.USA 105: 10360

  • DOI: 10.1073/pnas.0805326105

  • PubMed Abstract: 
  • The tumor suppressor p53 is mutationally inactivated in approximately 50% of human cancers. Approximately one-third of the mutations lower the melting temperature of the protein, leading to its rapid denaturation. Small molecules that bind to those m ...

    The tumor suppressor p53 is mutationally inactivated in approximately 50% of human cancers. Approximately one-third of the mutations lower the melting temperature of the protein, leading to its rapid denaturation. Small molecules that bind to those mutants and stabilize them could be effective anticancer drugs. The mutation Y220C, which occurs in approximately 75,000 new cancer cases per annum, creates a surface cavity that destabilizes the protein by 4 kcal/mol, at a site that is not functional. We have designed a series of binding molecules from an in silico analysis of the crystal structure using virtual screening and rational drug design. One of them, a carbazole derivative (PhiKan083), binds to the cavity with a dissociation constant of approximately 150 muM. It raises the melting temperature of the mutant and slows down its rate of denaturation. We have solved the crystal structure of the protein-PhiKan083 complex at 1.5-A resolution. The structure implicates key interactions between the protein and ligand and conformational changes that occur on binding, which will provide a basis for lead optimization. The Y220C mutant is an excellent "druggable" target for developing and testing novel anticancer drugs based on protein stabilization. We point out some general principles in relationships between binding constants, raising of melting temperatures, and increase of protein half-lives by stabilizing ligands.


    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

    Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 0QH, United Kingdom.




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
P83
Query on P83

Download SDF File 
Download CCD File 
B
1-(9-ethyl-9H-carbazol-3-yl)-N-methylmethanamine
C16 H18 N2
LBPNOEAFWYTTEB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P83Kd: 150000 nM BINDINGMOAD
P83Kd: 125000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.093α = 90.00
b = 71.234β = 90.00
c = 105.207γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance