MolNFT v1 · #153026 · protein
Ciclopirox inhibits hepatitis B virus secretion by blocking capsid assembly
6J10 · Capsid protein: “Ciclopirox inhibits hepatitis B virus secretion by blocking capsid assembly”. X-ray diffraction, 1 ligand (B4O), 6 pockets (best druggability 0.68). MolNFT v1 #153026 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6J10
- Type
- protein
- Length
- 846 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Ligands
- B4O
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Capsid protein | protein | 141 | 70% helix, 0% strand | P03147 |
Ligands and binding sites
- B4O · 6-cyclohexyl-4-methyl-1-oxidanyl-pyridin-2-one · ligand · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.68 | 0.88 | 26 | empty |
| 2 | 151 | 0.68 | 0.88 | 28 | empty |
| 3 | 241 | 0.67 | 0.83 | 32 | empty |
| 4 | 273 | 0.66 | 0.82 | 38 | empty |
| 5 | 140 | 0.66 | 0.87 | 26 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2057 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1996 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1979 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 568 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 494 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6J10 · Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly · 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
- Every structure of UniProt P03147
- Elsewhere: RCSB PDB 6J10 · PDBe 6J10 · UniProt P03147
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