Research workbench
Crystal structure of the human CB1 in complex with agonist AM11542
Analyse Crystal structure of the human CB1 in complex with agonist AM11542 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XRA
- Type
- protein
- Length
- 428 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
- OLA, FMN, 8D3, CLR
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cannabinoid receptor 1,FLAVODOXIN,CANNABINOID receptor 1 | protein | 428 | 67% helix, 9% strand | P21554, P00323 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 2 copies · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- 8D3 · (6aR,10aR)-3-(8-bromanyl-2-methyl-octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.86 | 0.96 | 39 | 8D3 |
| 2 | 396 | 0.60 | 0.76 | 35 | OLC |
| 3 | 95 | 0.42 | 0.78 | 25 | FMN |
| 4 | 81 | 0.40 | 0.77 | 13 | empty |
| 5 | 66 | 0.27 | 0.72 | 15 | OLA |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5XRA · Crystal structure of the human CB1 in complex with agonist AM11542 · 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 5XRA · PDBe 5XRA · UniProt P21554 · UniProt P00323
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