5A7B

Structure of the p53 cancer Y220C bound to the stabilizing small molecule PhiKan5211


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere.

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

(2015) ACS Chem Biol 10: 2725

  • DOI: 10.1021/acschembio.5b00515
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bioisosteric replacements are widely used in medicinal chemistry to improve physicochemical and ADME properties of molecules while retaining or improving affinity. Here, using the p53 cancer mutant Y220C as a test case, we investigate both computatio ...

    Bioisosteric replacements are widely used in medicinal chemistry to improve physicochemical and ADME properties of molecules while retaining or improving affinity. Here, using the p53 cancer mutant Y220C as a test case, we investigate both computationally and experimentally whether an ethynyl moiety is a suitable bioisostere to replace iodine in ligands that form halogen bonds with the protein backbone. This bioisosteric transformation is synthetically feasible via Sonogashira cross-coupling. In our test case of a particularly strong halogen bond, replacement of the iodine with an ethynyl group resulted in a 13-fold affinity loss. High-resolution crystal structures of the two analogues in complex with the p53-Y220C mutant enabled us to correlate the different affinities with particular features of the binding site and subtle changes in ligand binding mode. In addition, using QM calculations and analyzing the PDB, we provide general guidelines for identifying cases where such a transformation is likely to improve ligand recognition.


    Organizational Affiliation

    Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen , Sand 1, 72076 Tübingen, 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KMN
Query on KMN

Download CCD File 
A, B
2-[[4-(diethylamino)piperidin-1-yl]methyl]-6-ethynyl-4-(3-phenoxyprop-1-ynyl)phenol
C27 H32 N2 O2
WYIKILSZEONLKD-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 %)
KMNKd:  271000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.12α = 90
b = 71.111β = 90
c = 105.114γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-07-03 
  • Released Date: 2015-09-30 
  • Deposition Author(s): Joerger, A.C.

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    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