Research workbench
Structural determinants of activation and biased agonism at the 5-HT2B receptor
Analyse Structural determinants of activation and biased agonism at the 5-HT2B receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DS0
- Type
- protein
- Length
- 368 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5HT2B receptor, bril chimera
- UniProt
- P41595, P0ABE7
- Ligands
- CLR, H8M
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5HT2B receptor, bril chimera | protein | 368 | 81% helix, 0% strand | P41595, P0ABE7 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- H8M · (1S)-1-[(2-chloro-3,4-dimethoxyphenyl)methyl]-6-methyl-2,3,4,9-tetrahydro-1H-beta-carboline · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.78 | 0.87 | 41 | H8M |
| 2 | 357 | 0.65 | 0.79 | 42 | OLC, PEG |
| 3 | 240 | 0.57 | 0.78 | 26 | empty |
| 4 | 90 | 0.35 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6DS0 · Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P41595 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2B (P41595) · a predicted model of the same protein · chain A against A, TM-score 0.82
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.24
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 P41595
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6DS0 · PDBe 6DS0 · UniProt P41595 · UniProt P0ABE7
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