X-ray structure of compound 15 bound to hdmx: structural states of HDM2 and hdmx: X-ray elucidation of adaptations and binding interactions for different chemical compound classes

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).

Ligands and binding sites

• O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 4 copies · chains A, B
• HRT · (4~{S})-4-(4-chlorophenyl)-5-[(1~{S})-1-(3-chlorophenyl)ethyl]-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 111 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6Q9W · X-ray structure of compound 15 bound to HdmX: Structural states of Hdm2 and HdmX: X-ray… · the same entry in another collection · chain A against A, TM-score 1.00
• O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O15151
• Elsewhere: RCSB PDB 6Q9W · PDBe 6Q9W · UniProt O15151