Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).

Ligands and binding sites

• 76J · [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 6 copies · chains A, B
• SCN · Thiocyanate ion · ion · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 454 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5LT6 · Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9BYW2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 Q9BYW2
• Elsewhere: RCSB PDB 5LT6 · PDBe 5LT6 · UniProt Q9BYW2