Structure of the p53 cancer mutant Y220C in complex with 2-hydroxy-3, 5-diiodo-4-(1H-pyrrol-1-yl)benzoic acid

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.str.2015.10.016
  • Primary Citation of Related Structures:  
    5AB9, 5ABA, 5AOI, 5AOJ, 5AOK, 5AOL, 5AOM

  • 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 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. Electronic address: andreas.joerger@gmx.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
219Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
Y0V Binding MOAD:  5AOJ Kd: 2.10e+4 (nM) from 1 assay(s)
BindingDB:  5AOJ Kd: 2.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.216α = 90
b = 71.108β = 90
c = 105.353γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description