MolNFT v1 · #165255 · protein
Crystal structure of the orexin-1 receptor in complex with act-462206
6TP4 · Orexin receptor type 1: “Crystal structure of the orexin-1 receptor in complex with act-462206”. X-ray diffraction, 4 ligands (SOG, PGW, NRZ), 9 pockets (best druggability 0.88). MolNFT v1 #165255 on GenesisL1: 3D structure, binding…
- PDB
- 6TP4
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orexin receptor type 1
- UniProt
- O43613
- Ligands
- SOG, PGW, NRZ, SO4
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orexin receptor type 1 | protein | 298 | 83% helix, 4% strand | O43613 |
| B | Orexin receptor type 1 | protein | 300 | 79% helix, 3% strand | O43613 |
Ligands and binding sites
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 5 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
- NRZ · (2~{S})-~{N}-(3,5-dimethylphenyl)-1-(4-methoxyphenyl) sulfonyl-pyrrolidine-2-carboxamide · ligand · chains A
- 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.88 | 0.88 | 102 | PGW, SOG |
| 2 | 697 | 0.83 | 0.86 | 48 | NRZ |
| 3 | 691 | 0.82 | 0.86 | 47 | empty |
| 4 | 166 | 0.48 | 0.77 | 27 | SO4 |
| 5 | 163 | 0.46 | 0.76 | 29 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1065 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6TP4 · Crystal structure of the Orexin-1 receptor in complex with ACT-462206 · 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 6TP4 · PDBe 6TP4 · UniProt O43613
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