Crystal structure of HSIRT3 in complex with a specific agonist amiodarone hydrochloride

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).

Ligands and binding sites

• BBI · (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone · ligand · 2 copies · chains A, H
• NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, H
• FDL · N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide · ligand · 2 copies · chains D, H, A, C
• ZN · Zinc ion · metal · 2 copies · chains A, H
• MG · Magnesium ion · metal · 2 copies · chains A, H
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains H

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

5 interfaces between chains.

• A–H · 291 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 203 Ų buried · 1 hydrogen bond · protein-protein
• D–H · 197 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
• H–C · 10 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 5H4D · Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain H against A, TM-score 0.95

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 Q9NTG7
• Elsewhere: RCSB PDB 5H4D · PDBe 5H4D · UniProt Q9NTG7