Urea-based foldamer inhibitor chimera C2 in complex with ASF1 histone chaperone

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 52% strand (DSSP).

Ligands and binding sites

• QQB · ~{N}-[(2~{S})-2-azanyl-3-naphthalen-1-yl-propyl]methanamide · ligand · 2 copies · chains C, D
• URL · [(2~{S})-2-azanyl-4-methyl-pentyl]carbamic acid · ligand · 2 copies · chains A, C, B, D
• QQ8 · (4~{S})-4-azanyl-5-formamido-pentanamide · ligand · 2 copies · chains C, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 9 copies · chains A, B, C, D

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

3 interfaces between chains.

• B–D · 544 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 526 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 246 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

• 6ZUF · Urea-based Foldamer Inhibitor chimera C2 in complex with ASF1 Histone chaperone · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y294 · AlphaFold monomer V2.0 prediction for histone chaperone ASF1A (Q9Y294) · 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 Q9Y294
• Elsewhere: RCSB PDB 6ZUF · PDBe 6ZUF · UniProt Q9Y294