The 2.3A crystal structure of humanized xenopus MDM2 with RO5545353

Structure

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

Ligands and binding sites

• 20W · (2S,3R,4R,5R)-N-(4-carbamoyl-2-methoxyphenyl)-2'-chloro-4-(3-chloro-2-fluorophenyl)-2-(2,2-dimethylpropyl)-5'-oxo-4',5'-dihydrospiro[pyrrolidine-3,6'-thieno[3,2-b]pyrrole]-5-carboxamide · ligand · 3 copies · chains A, C, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, C, 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, 1 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–B · 389 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 154 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 4LWV · The 2.3A Crystal Structure of Humanized Xenopus MDM2 with RO5545353 · 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 0.95

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 4LWV · PDBe 4LWV · UniProt P56273