Crystal structure of HDM2 in complex with a C-terminal triurea capped peptide chimera foldamer.

Structure

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

Ligands and binding sites

• G2B · 1-[(2~{R},3~{S})-2-azanyl-3-oxidanyl-butyl]urea · ligand · 4 copies · chains A, B, C, D
• UCV · 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea · ligand · 2 copies · chains B, C, A, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 564 Ų buried · 12 hydrogen bonds · protein-protein
• B–C · 413 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 396 Ų buried · 2 hydrogen bonds · protein-protein
• A–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 249 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6HFA · Crystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera… · 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 Q00987
• Elsewhere: RCSB PDB 6HFA · PDBe 6HFA · UniProt Q00987