MolNFT v1 · #8521 · protein
Structures of human oxidosqualene cyclase inhibitors bound to an homologous enzyme
1H39 · Squalene--hopene cyclase: “Structures of human oxidosqualene cyclase inhibitors bound to an homologous enzyme”. X-ray diffraction, 1 ligand (R03), 20 pockets (best druggability 0.87). MolNFT v1 #8521 on GenesisL1: 3D structure…
- PDB
- 1H39
- Type
- protein
- Length
- 1,857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squalene--hopene cyclase
- EC
- 5.4.99.17
- UniProt
- P33247
- Ligands
- R03
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Squalene--hopene cyclase (EC 5.4.99.17) | protein | 619 | 53% helix, 3% strand | P33247 |
Ligands and binding sites
- R03 · Allyl-{6-[3-(4-bromo-phenyl)-1-methyl-1H-indazol-6-yl]oxy}hexyl)-N-methylamine · ligand · 3 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.87 | 0.95 | 55 | R03 |
| 2 | 391 | 0.86 | 0.94 | 52 | R03 |
| 3 | 396 | 0.86 | 0.94 | 60 | R03 |
| 4 | 91 | 0.75 | 0.96 | 19 | empty |
| 5 | 236 | 0.67 | 0.84 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 573 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1H39 · Structures of Human Oxidosqualene Cyclase Inhibitors Bound to an Homologous Enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- P33247 · AlphaFold monomer V2.0 prediction for squalene--hopene cyclase (P33247) · a predicted model of the same protein · 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
- Every structure of UniProt P33247
- Elsewhere: RCSB PDB 1H39 · PDBe 1H39 · UniProt P33247
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