MolNFT v1 · #160740 · protein
Crystal structure of the active delta opioid receptor in complex with the small molecule agonist dpi-287
6PT3: “Crystal structure of the active delta opioid receptor in complex with the small molecule agonist dpi-287”. X-ray diffraction, 1 ligand (OWY), 10 pockets (best druggability 0.78). MolNFT v1 #160740 on GenesisL1: 3D structure, binding…
- PDB
- 6PT3
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta opioid receptor
- Ligands
- OWY
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta opioid receptor | protein | 397 | 79% helix, 4% strand | — |
| B | Delta opioid receptor | protein | 355 | 81% helix, 4% strand | — |
Ligands and binding sites
- OWY · 4-[(R)-[(2S,5R)-4-benzyl-2,5-dimethylpiperazin-1-yl](3-hydroxyphenyl)methyl]-N,N-diethylbenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 46 | OWY |
| 2 | 1090 | 0.76 | 0.78 | 66 | OWY |
| 3 | 289 | 0.64 | 0.80 | 31 | empty |
| 4 | 247 | 0.62 | 0.80 | 31 | empty |
| 5 | 279 | 0.58 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1259 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PT3 · Crystal structure of the active delta opioid receptor in complex with the small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6PT3 · PDBe 6PT3
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