Hdmx (14-111; C17S) complexed with compound 13 at 2.1A; 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, 16% strand (DSSP).

Ligands and binding sites

• O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 5 copies · chains A, B, C, D
• HUE · 6-chloranyl-3-[3-[(1~{S})-1-(4-chlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-~{N}-[2-(4-cyclohexylpiperazin-1-yl)ethyl]-1~{H}-indole-2-carboxamide · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
• GOL · Glycerol · additive · chains B

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

Pockets

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

Interfaces

3 interfaces between chains.

• B–C · 463 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 393 Ų buried · 8 hydrogen bonds · protein-protein
• C–D · 361 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 6Q9Q · HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 13 AT 2.1A; Structural states of Hdm2 and… · 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 C 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 6Q9Q · PDBe 6Q9Q · UniProt O15151