MolNFT v1 · #138659 · protein
Crystal structure of human orexin 2 receptor bound to the selective antagonist empa determined by the synchrotron light source at spring- 8.
5WQC · Orexin receptor type 2,GLGA glycogen SYNTHASE,OREXIN…: “Crystal structure of human orexin 2 receptor bound to the selective antagonist empa determined by the…”. X-ray diffraction, 2 ligands (OLA, 7MA), 4 pockets (best druggability…
- PDB
- 5WQC
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orexin receptor type 2,GLGA glycogen SYNTHASE,OREXIN receptor type 2
- UniProt
- O43614, Q9V2J8
- Ligands
- OLA, 7MA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orexin receptor type 2,GLGA glycogen SYNTHASE,OREXIN receptor type 2 | protein | 499 | 68% helix, 8% strand | O43614, Q9V2J8 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 5 copies · chains A
- 7MA · N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl) sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide · ligand · chains A
- 1PE · Pentaethylene glycol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.82 | 0.86 | 48 | 7MA, 1PE |
| 2 | 156 | 0.47 | 0.77 | 25 | empty |
| 3 | 134 | 0.46 | 0.77 | 25 | empty |
| 4 | 149 | 0.43 | 0.75 | 30 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5WQC · Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA… · the same entry in another collection · chain A against A, TM-score 1.00
- O43614 · AlphaFold monomer V2.0 prediction for orexin receptor type 2 (O43614) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 O43614
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 5WQC · PDBe 5WQC · UniProt O43614 · UniProt Q9V2J8
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