Human SIRT5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).

Ligands and binding sites

• BV8 · 3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3, 4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino) hexyl]carbonimidoyl]amino]propanoic acid · ligand · 4 copies · chains A, D, B, C
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
• BU2 · 1,3-butanediol · additive · 8 copies · chains A, B, C, D
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–D · 527 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 490 Ų buried · 4 hydrogen bonds · protein-protein
• B–D · 357 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 6EQS · Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29 · the same entry in another collection · chain D against D, TM-score 1.00
• Q9NXA8 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain B 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 Q9NXA8
• Elsewhere: RCSB PDB 6EQS · PDBe 6EQS · UniProt Q9NXA8