Research workbench
High-resolution crystal structure of the human CB1 cannabinoid receptor
Analyse High-resolution crystal structure of the human CB1 cannabinoid receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U09
- Type
- protein
- Length
- 478 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cannabinoid receptor 1,GLGA glycogen synthase
- UniProt
- P21554, Q9V2J8
- Ligands
- 7DY, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cannabinoid receptor 1,GLGA glycogen synthase | protein | 478 | 67% helix, 7% strand | P21554, Q9V2J8 |
Ligands and binding sites
- 7DY · N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.81 | 0.88 | 62 | 7DY |
| 2 | 180 | 0.48 | 0.75 | 32 | empty |
| 3 | 64 | 0.43 | 0.81 | 17 | PEG |
| 4 | 76 | 0.42 | 0.79 | 11 | SO4 |
| 5 | 106 | 0.39 | 0.76 | 21 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5U09 · High-resolution crystal structure of the human CB1 cannabinoid receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P21554 · AlphaFold monomer V2.0 prediction for cannabinoid receptor 1 (P21554) · a predicted model of the same protein · chain A against A, TM-score 0.55
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 P21554
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 5U09 · PDBe 5U09 · UniProt P21554 · UniProt Q9V2J8
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