5AOM

Structure of the p53 cancer mutant Y220C with bound small molecule PhiKan883

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Exploiting Transient Protein States for the Design of Small-Molecule Stabilizers of Mutant P53.

Joerger, A.C., Bauer, M.R., Wilcken, R., Baud, M.G.J., Harbrecht, H., Exner, T.E., Boeckler, F.M., Spencer, J., Fersht, A.R.

(2015) Structure 23: 2246

  • DOI: 10.1016/j.str.2015.10.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The destabilizing p53 cancer mutation Y220C creates an extended crevice on the surface of the protein that can be targeted by small-molecule stabilizers. Here, we identify different classes of small molecules that bind to this crevice and determine t ...

    The destabilizing p53 cancer mutation Y220C creates an extended crevice on the surface of the protein that can be targeted by small-molecule stabilizers. Here, we identify different classes of small molecules that bind to this crevice and determine their binding modes by X-ray crystallography. These structures reveal two major conformational states of the pocket and a cryptic, transiently open hydrophobic subpocket that is modulated by Cys220. In one instance, specifically targeting this transient protein state by a pyrrole moiety resulted in a 40-fold increase in binding affinity. Molecular dynamics simulations showed that both open and closed states of this subsite were populated at comparable frequencies along the trajectories. Our data extend the framework for the design of high-affinity Y220C mutant binders for use in personalized anticancer therapy and, more generally, highlight the importance of implementing protein dynamics and hydration patterns in the drug-discovery process.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, 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 UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
GTEx  ENSG00000141510
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FY8
Query on FY8
Download CCD File 
A, B
N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide
C12 H15 Cl N2 O2
GIWLSSKLZAAODK-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FY8Kd:  1270000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.16α = 90
b = 71.27β = 90
c = 105.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-05-15
    Changes: Data collection, Experimental preparation