MolNFT v1 · #75139 · protein
HCV NS5B with a bound quinolone inhibitor
3PHE · HCV encoded nonstructural 5B protein: “HCV NS5B with a bound quinolone inhibitor”. X-ray diffraction, 1 ligand (C9A), 20 pockets (best druggability 0.79). MolNFT v1 #75139 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3PHE
- Type
- protein
- Length
- 2,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV encoded nonstructural 5B protein
- UniProt
- D0PY27
- Ligands
- C9A
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HCV encoded nonstructural 5B protein | protein | 558 | 48% helix, 16% strand | D0PY27 |
Ligands and binding sites
- C9A · 4-chlorobenzyl 6-fluoro-7-(4-methylpiperazin-1-yl)-1-[4-(methylsulfonyl)benzyl]-4-oxo-1,4-dihydroquinoline-3-carboxylate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.79 | 0.81 | 77 | empty |
| 2 | 954 | 0.79 | 0.81 | 80 | empty |
| 3 | 969 | 0.79 | 0.81 | 76 | empty |
| 4 | 933 | 0.79 | 0.81 | 77 | empty |
| 5 | 142 | 0.56 | 0.82 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 267 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PHE · HCV NS5B with a bound quinolone inhibitor · 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 D0PY27
- Elsewhere: RCSB PDB 3PHE · PDBe 3PHE · UniProt D0PY27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.