MolNFT v1 · #121060 · protein
Human sigma-1 receptor bound to PD144418
5HK1 · Sigma non-opioid intracellular receptor 1: “Human sigma-1 receptor bound to PD144418”. X-ray diffraction, 2 ligands (61W, SO4), 9 pockets (best druggability 0.85). MolNFT v1 #121060 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HK1
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sigma non-opioid intracellular receptor 1
- UniProt
- Q99720
- Ligands
- 61W, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sigma non-opioid intracellular receptor 1 | protein | 212 | 42% helix, 29% strand | Q99720 |
| B | Sigma non-opioid intracellular receptor 1 | protein | 219 | 37% helix, 28% strand | Q99720 |
| C | Sigma non-opioid intracellular receptor 1 | protein | 219 | 40% helix, 28% strand | Q99720 |
Ligands and binding sites
- 61W · 3-(4-methylphenyl)-5-(1-propyl-3,6-dihydro-2H-pyridin-5-yl)-1,2-oxazole · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.85 | 0.97 | 37 | 61W |
| 2 | 231 | 0.84 | 0.96 | 38 | 61W |
| 3 | 210 | 0.83 | 0.96 | 36 | 61W |
| 4 | 159 | 0.79 | 0.95 | 55 | SO4 |
| 5 | 167 | 0.44 | 0.74 | 21 | OLC |
Interfaces
3 interfaces between chains.
- A–C · 1019 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1019 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1018 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 Q99720
- Elsewhere: RCSB PDB 5HK1 · PDBe 5HK1 · UniProt Q99720
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