3ZME image
Deposition Date 2013-02-07
Release Date 2013-05-08
Last Version Date 2024-05-08
Entry Detail
PDB ID:
3ZME
Keywords:
Title:
Structure of the p53 core domain mutant Y220C bound to the small molecule PhiKan7242
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.35 Å
R-Value Free:
0.17
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Cellular tumor antigen p53
Gene (Uniprot):TP53
Mutations:Y220C
Chain IDs:A, B
Chain Length:219
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Small molecule induced reactivation of mutant p53 in cancer cells.
Nucleic Acids Res. 41 6034 6044 (2013)
PMID: 23630318 DOI: 10.1093/nar/gkt305

Abstact

The p53 cancer mutant Y220C is an excellent paradigm for rescuing the function of conformationally unstable p53 mutants because it has a unique surface crevice that can be targeted by small-molecule stabilizers. Here, we have identified a compound, PK7088, which is active in vitro: PK7088 bound to the mutant with a dissociation constant of 140 μM and raised its melting temperature, and we have determined the binding mode of a close structural analogue by X-ray crystallography. We showed that PK7088 is biologically active in cancer cells carrying the Y220C mutant by a battery of tests. PK7088 increased the amount of folded mutant protein with wild-type conformation, as monitored by immunofluorescence, and restored its transcriptional functions. It induced p53-Y220C-dependent growth inhibition, cell-cycle arrest and apoptosis. Most notably, PK7088 increased the expression levels of p21 and the proapoptotic NOXA protein. PK7088 worked synergistically with Nutlin-3 on up-regulating p21 expression, whereas Nutlin-3 on its own had no effect, consistent with its mechanism of action. PK7088 also restored non-transcriptional apoptotic functions of p53 by triggering nuclear export of BAX to the mitochondria. We suggest a set of criteria for assigning activation of p53.

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Primary Citation of related structures