Structural basis of reactivation of oncogenic P53 mutants by a small molecule: methylene quinuclidinone (mq). human P53DBD-R273C mutant bound to mq: R273C-mq (II)

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 35% strand (DSSP).

Ligands and binding sites

• QNN · (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one · ligand · 6 copies · chains A, B, C, D
• QN8 · (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one · ligand · chains B
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–D · 533 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 530 Ų buried · 5 hydrogen bonds · protein-protein
• A–B · 496 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 174 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (covalent ligand).

Compared structures

• 7B4C · Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P04637
• Elsewhere: RCSB PDB 7B4C · PDBe 7B4C · UniProt P04637