4AGO | pdb_00004ago

Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5174


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.217 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P74Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant P53.

Wilcken, R.Liu, X.Zimmermann, M.O.Rutherford, T.J.Fersht, A.R.Joerger, A.C.Boeckler, F.M.

(2012) J Am Chem Soc 134: 6810

  • DOI: https://doi.org/10.1021/ja301056a
  • Primary Citation of Related Structures:  
    4AGL, 4AGM, 4AGN, 4AGO, 4AGP, 4AGQ

  • PubMed Abstract: 

    The destabilizing p53 cancer mutation Y220C creates a druggable surface crevice. We developed a strategy exploiting halogen bonding for lead discovery to stabilize the mutant with small molecules. We designed halogen-enriched fragment libraries (HEFLibs) as starting points to complement classical approaches. From screening of HEFLibs and subsequent structure-guided design, we developed substituted 2-(aminomethyl)-4-ethynyl-6-iodophenols as p53-Y220C stabilizers. Crystal structures of their complexes highlight two key features: (i) a central scaffold with a robust binding mode anchored by halogen bonding of an iodine with a main-chain carbonyl and (ii) an acetylene linker, enabling the targeting of an additional subsite in the crevice. The best binders showed induction of apoptosis in a human cancer cell line with homozygous Y220C mutation. Our structural and biophysical data suggest a more widespread applicability of HEFLibs in drug discovery.


  • Organizational Affiliation

    Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELLULAR TUMOR ANTIGEN P53
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.217 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.05α = 90
b = 71.13β = 90
c = 105.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P74Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Other
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description