Research workbench
Crystal structure of the orexin-1 receptor in complex with sb-408124
Analyse Crystal structure of the orexin-1 receptor in complex with sb-408124 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TQ9
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orexin receptor type 1
- UniProt
- O43613
- Ligands
- SOG, NVN, PGW, SO4
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orexin receptor type 1 | protein | 304 | 83% helix, 3% strand | O43613 |
| B | Orexin receptor type 1 | protein | 302 | 81% helix, 3% strand | O43613 |
Ligands and binding sites
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 10 copies · chains A, B
- NVN · 1-[6,8-bis(fluoranyl)-2-methyl-quinolin-4-yl]-3-[4-(dimethylamino)phenyl]urea · ligand · 3 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.88 | 0.89 | 87 | SOG, PGW |
| 2 | 804 | 0.83 | 0.86 | 55 | NVN |
| 3 | 843 | 0.83 | 0.85 | 60 | NVN |
| 4 | 178 | 0.54 | 0.79 | 25 | SO4 |
| 5 | 110 | 0.41 | 0.76 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6TQ9 · Crystal structure of the Orexin-1 receptor in complex with SB-408124 · 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 B 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 6TQ9 · PDBe 6TQ9 · UniProt O43613
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