8A32

p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


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Literature

Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic p53 Mutant Y220C.

Stephenson Clarke, J.R.Douglas, L.R.Duriez, P.J.Balourdas, D.I.Joerger, A.C.Khadiullina, R.Bulatov, E.Baud, M.G.J.

(2022) Acs Pharmacol Transl Sci 5: 1169-1180

  • DOI: https://doi.org/10.1021/acsptsci.2c00164
  • Primary Citation of Related Structures:  
    8A31, 8A32

  • PubMed Abstract: 

    The tumor suppressor protein p53 is inactivated in the majority of human cancers and remains a prime target for developing new drugs to reactivate its tumor suppressing activity for anticancer therapies. The oncogenic p53 mutant Y220C accounts for approximately 125,000 new cancer cases per annum and is one of the most prevalent p53 mutants overall. It harbors a narrow, mutationally induced pocket at the surface of the DNA-binding domain that destabilizes p53, leading to its rapid denaturation and aggregation. Here, we present the structure-guided development of high-affinity small molecules stabilizing p53-Y220C in vitro , along with the synthetic routes developed in the process, in vitro structure-activity relationship data, and confirmation of their binding mode by protein X-ray crystallography. We disclose two new chemical probes displaying sub-micromolar binding affinity in vitro , marking an important milestone since the discovery of the first small-molecule ligand of Y220C in 2008. New chemical probe JC744 displayed a K d = 320 nM, along with potent in vitro protein stabilization. This study, therefore, represents a significant advance toward high-affinity Y220C ligands for clinical evaluation.


  • Organizational Affiliation

    Cancer Research UK, Somers Building, University Hospital Southampton, Tremona Road, Southampton SO16 6YD, United Kingdom.


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 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KVA (Subject of Investigation/LOI)
Query on KVA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic acid
C11 H5 F2 I2 N O3
FESMMSZGNQNLCH-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.119α = 90
b = 71.072β = 90
c = 105.315γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyJO 1473/1-3

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description