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: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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This is version 1.3 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 U S A 105: 10360

  • DOI: 10.1073/pnas.0805326105
  • Primary Citation of Related Structures:  
    2VUK

  • 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 mutants and stabilize them could be effective anticancer drugs ...

    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 U S A 103: 15056

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULAR TUMOR ANTIGEN P53A, B219Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P83 (Subject of Investigation/LOI)
Query on P83

Download Ideal Coordinates CCD File 
D [auth B]1-(9-ethyl-9H-carbazol-3-yl)-N-methylmethanamine
C16 H18 N2
LBPNOEAFWYTTEB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P83 Binding MOAD:  2VUK Kd: 1.25e+5 (nM) from 1 assay(s)
PDBBind:  2VUK Kd: 1.25e+5 (nM) from 1 assay(s)
BindingDB:  2VUK Kd: 1.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.093α = 90
b = 71.234β = 90
c = 105.207γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other