Human sigma-1 receptor bound to PD144418

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 29% strand (DSSP).

Ligands and binding sites

• 61W · 3-(4-methylphenyl)-5-(1-propyl-3,6-dihydro-2H-pyridin-5-yl)-1,2-oxazole · ligand · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains A, C

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1019 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 1019 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 1018 Ų buried · 15 hydrogen bonds · protein-protein

Compared structures

• 5HK1 · Human sigma-1 receptor bound to PD144418 · the same entry in another collection · chain A against A, TM-score 1.00
• Q99720 · AlphaFold monomer V2.0 prediction for sigma non-opioid intracellular receptor 1 (Q99720) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q99720
• Elsewhere: RCSB PDB 5HK1 · PDBe 5HK1 · UniProt Q99720