Zebrafish SIRT5 in complex with stalled bicyclic intermediate of inhibitory compound 10

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Ligands and binding sites

• BJW · 4-[(2~{R},3~{A}~{R},5~{R},6~{R},6~{A}~{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]-2-[[(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]amino]-6-oxidanyl-3~{A},5,6,6~{A}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]butanoic acid · ligand · chains A
• ZN · Zinc ion · metal · chains A
• DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

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

Compared structures

• 6ENX · Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10 · the same entry in another collection · chain A against A, TM-score 1.00
• Q6DHI5 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q6DHI5
• Elsewhere: RCSB PDB 6ENX · PDBe 6ENX · UniProt Q6DHI5