Research workbench
Crystal structure of the human CB1 in complex with agonist AM841
Analyse Crystal structure of the human CB1 in complex with agonist AM841 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XR8
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cannabinoid receptor 1,FLAVODOXIN,CANNABINOID receptor 1
- UniProt
- P21554, P00323
- Ligands
- FMN, 8D0, CLR
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cannabinoid receptor 1,FLAVODOXIN,CANNABINOID receptor 1 | protein | 431 | 63% helix, 8% strand | P21554, P00323 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- 8D0 · (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.86 | 0.95 | 40 | 8D0 |
| 2 | 435 | 0.61 | 0.76 | 46 | empty |
| 3 | 95 | 0.46 | 0.79 | 11 | empty |
| 4 | 75 | 0.41 | 0.79 | 22 | FMN |
| 5 | 50 | 0.35 | 0.78 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5XR8 · Crystal structure of the human CB1 in complex with agonist AM841 · 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 0.65
- P00323 · AlphaFold monomer V2.0 prediction for flavodoxin (P00323) · a predicted model of the same protein · chain A against A, TM-score 0.34
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 P00323
- Elsewhere: RCSB PDB 5XR8 · PDBe 5XR8 · UniProt P21554 · UniProt P00323
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.