8RBC
p53-Y220C Core Domain Covalently Bound to 3-amino-5-chloropyrazine-2,6-dicarbonitrile Soaked at 5 mM
Summary for 8RBC
| Entry DOI | 10.2210/pdb8rbc/pdb |
| Related | 8RBA 8RBB |
| Descriptor | Cellular tumor antigen p53, 3-azanylpyrazine-2,6-dicarbonitrile, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (6 entities in total) |
| Functional Keywords | covalent, snar, stabilization, cell cycle |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 2 |
| Total formula weight | 50448.84 |
| Authors | Stahlecker, J.,Klett, T.,Stehle, T.,Boeckler, F.M. (deposition date: 2023-12-04, release date: 2024-11-27, Last modification date: 2025-01-01) |
| Primary citation | Klett, T.,Stahlecker, J.,Jaag, S.,Masberg, B.,Knappe, C.,Lammerhofer, M.,Coles, M.,Stehle, T.,Boeckler, F.M. Covalent Fragments Acting as Tyrosine Mimics for Mutant p53-Y220C Rescue by Nucleophilic Aromatic Substitution. Acs Pharmacol Transl Sci, 7:3984-3999, 2024 Cited by PubMed Abstract: The tumor suppressor p53 is frequently mutated in human cancers. The Y220C mutant is the ninth most common p53 cancer mutant and is classified as a structural mutant, as it leads to strong thermal destabilization and degradation by creating a solvent-accessible hydrophobic cleft. To identify small molecules that thermally stabilize p53, we employed DSF to screen SAr-type electrophiles from our covalent fragment library (CovLib) for binding to different structural (Y220C, R282W) and DNA contact (R273H) mutants of p53. The reactive fragments SN001, SN006, and SN007 were detected to specifically stabilize Y220C, indicating the arylation of Cys220 in the mutational cleft, as confirmed by X-ray crystallography. The fragments occupy the central cavity and mimic the ring system of the WT tyrosine lost by the mutation. Surpassing previously reported noncovalent ligands, SN001 stabilized T-p53C-Y220C concentration-dependently up to 4.45 °C and, due to its small size, represents a promising starting point for optimization. PubMed: 39698266DOI: 10.1021/acsptsci.4c00414 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.06 Å) |
Structure validation
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