Research workbench
Discovery of an irreversible HCV NS5B polymerase inhibitor
Analyse Discovery of an irreversible HCV NS5B polymerase inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZ4
- Type
- protein
- Length
- 1,123 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- O92972
- Ligands
- 2F3, PO4
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 563 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 560 | 48% helix, 15% strand | O92972 |
Ligands and binding sites
- 2F3 · 1-[(2-chloroquinolin-3-yl)methyl]-6-fluoro-5-methyl-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.80 | 0.82 | 78 | 2F3 |
| 2 | 1112 | 0.80 | 0.81 | 86 | 2F3 |
| 3 | 109 | 0.50 | 0.81 | 19 | empty |
| 4 | 119 | 0.46 | 0.78 | 21 | empty |
| 5 | 121 | 0.45 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 995 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4MZ4 · Discovery of an Irreversible HCV NS5B Polymerase 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 O92972
- Elsewhere: RCSB PDB 4MZ4 · PDBe 4MZ4 · UniProt O92972
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