8A92 image
Deposition Date 2022-06-27
Release Date 2022-11-09
Last Version Date 2024-01-31
Entry Detail
PDB ID:
8A92
Keywords:
Title:
p53-Y220C Core Domain in Complex with a Bromo-trifluoro-pyrazole-amine
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.37 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cellular tumor antigen p53
Gene (Uniprot):TP53
Mutagens:Y220C,M133L,V203A,N239Y,N268D
Chain IDs:A, B
Chain Length:219
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C.
Rsc Med Chem 13 1575 1586 (2022)
PMID: 36561072 DOI: 10.1039/d2md00246a

Abstact

The cellular tumor antigen p53 is a key component in cell cycle control. The mutation Y220C heavily destabilizes the protein thermally but yields a druggable crevice. We have screened the diversity-optimized halogen-enriched fragment library against T-p53C-Y220C with STD-NMR and DSF to identify hits, which we validated by 1H,15N-HSQC NMR. We could identify four hits binding in the Y220C cleft, one hit binding covalently and four hits binding to an uncharacterized binding site. Compound 1151 could be crystallized showing a flip of C220 and thus opening subsite 3. Additionally, 4482 was identified to alkylate cysteines. Data shows that the diversity-optimized HEFLib leads to multiple diverse hits. The identified scaffolds can be used to further optimize interactions with T-p53C-Y220C and increase thermal stability.

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Primary Citation of related structures