The 2.5A crystal structure of humanized xenopus MDM2 with RO5316533 - a pyrrolidine MDM2 inhibitor

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).

Ligands and binding sites

• 1OY · (3S,4R,5S)-3-(3-chloro-2-fluorophenyl)-4-(4-chloro-2-fluorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide · ligand · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 429 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 4JSC · The 2.5A crystal structure of humanized Xenopus MDM2 with RO5316533 - a pyrrolidine MDM2… · the same entry in another collection · chain A against A, TM-score 1.00
• P56273 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (P56273) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P56273
• Elsewhere: RCSB PDB 4JSC · PDBe 4JSC · UniProt P56273