Crystal structure of SMYD3 with SAM and EPZ028862

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Ligands and binding sites

• SAM · S-adenosylmethionine · ligand · chains A
• 8WD · N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Compared structures

• 5V37 · Crystal structure of SMYD3 with SAM and EPZ028862 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · a predicted model of the same protein · 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 Q9H7B4
• Elsewhere: RCSB PDB 5V37 · PDBe 5V37 · UniProt Q9H7B4