Crystal structure of the orexin-1 receptor in complex with suvorexant at 2.29 a resolution

Structure

x-ray diffraction · 2 distinct chains · 82% helix, 3% strand (DSSP).

Ligands and binding sites

• SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 43 copies · chains A, B
• SUV · [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-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
• NA · Sodium ion · metal · 2 copies · chains A, B
• PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B
• CIT · Citric acid · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1023 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 6TO7 · Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution · 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 0.96

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 O43613
• Elsewhere: RCSB PDB 6TO7 · PDBe 6TO7 · UniProt O43613