4AGQ

Structure of the p53 core domain mutant Y220C bound to the stabilizing small molecule PhiKan5196


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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
  • Structures With Same Primary Citation

  • 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 U S A 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: TP53P53
Find proteins for P04637 (Homo sapiens)
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P96
Query on P96

Download CCD File 
A, B
2-{[4-(diethylamino)piperidin-1-yl]methyl}-6-iodo-4-[3-(phenylamino)prop-1-yn-1-yl]phenol
C25 H32 I N3 O
IZUZDXSTWPMHFT-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 %)
P96Kd :  9700   nM  PDBBind
P96Kd:  9700   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.038α = 90
b = 71.242β = 90
c = 104.938γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation