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

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 26% strand (DSSP).

Ligands and binding sites

• 76K · [(2~{S},5~{R})-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]-(3-oxidanylpropyl)azanium · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A
• SCN · Thiocyanate ion · ion · 2 copies · chains A

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.

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 5LSZ · 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 A against A, TM-score 0.90

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 5LSZ · PDBe 5LSZ · UniProt Q9BYW2