Crystal structure of the orexin-1 receptor in complex with daridorexant

Structure

x-ray diffraction · 2 distinct chains · 79% helix, 3% strand (DSSP).

Ligands and binding sites

• SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 14 copies · chains A, B
• NS2 · [(2~{S})-2-(6-chloranyl-7-methyl-1~{H}-benzimidazol-2-yl)-2-methyl-pyrrolidin-1-yl]-[5-methoxy-2-(1,2,3-triazol-2-yl)phenyl]methanone · ligand · 2 copies · chains A, B
• PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1002 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 6TP3 · Crystal structure of the Orexin-1 receptor in complex with daridorexant · the same entry in another collection · chain A against A, TM-score 1.00
• O43613 · AlphaFold monomer V2.0 prediction for orexin receptor type 1 (O43613) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O43613
• Elsewhere: RCSB PDB 6TP3 · PDBe 6TP3 · UniProt O43613