4AGP

Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5176

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/ja301056a
  • Primary Citation of Related Structures:  

  • 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 (HEFL ...

    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.

    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: 

    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: 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
P51
Query on P51
Download SDF File 
Download CCD File 
A, B
2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-(3-phenoxyprop-1-yn-1-yl)phenol
C25 H31 I N2 O2
QHQZDNCRBPFORJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P51Kd: 20600 nM BINDINGMOAD
P51Kd: 20600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.080α = 90.00
b = 71.170β = 90.00
c = 104.980γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Other
  • Version 1.2: 2019-05-08
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Type: Data collection, Experimental preparation