Research workbench
Crystal structure of inactive 5-HT5AR in complex with AS2674723
Analyse Crystal structure of inactive 5-HT5AR in complex with AS2674723 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UM4
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 5A; Pgs
- UniProt
- P47898
- Ligands
- NN6
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-hydroxytryptamine receptor 5A | protein | 254 | 78% helix, 1% strand | P47898 |
| B | Pgs | protein | 199 | 46% helix, 15% strand | — |
Ligands and binding sites
- NN6 · ~{N}-[azanyl(azanylidene)methylidene]-5-fluoranyl-8-[2, 4,6-tris(fluoranyl)phenyl]-3,4-dihydro-1~{H}-isoquinoline-2-carboxamide · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.75 | 0.85 | 43 | NN6 |
| 2 | 710 | 0.72 | 0.78 | 48 | empty |
| 3 | 223 | 0.54 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 409 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7UM4 · Crystal structure of inactive 5-HT5AR in complex with AS2674723 · the same entry in another collection · chain A against A, TM-score 1.00
- P47898 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 5A (P47898) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P47898
- Elsewhere: RCSB PDB 7UM4 · PDBe 7UM4 · UniProt P47898
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