Research workbench
Crystal Structure of HCV NS5B Polymerase with a Novel Pyridazi Inhibitor
Analyse Crystal Structure of HCV NS5B Polymerase with a Novel Pyridazi Inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BR9
- Type
- protein
- Length
- 1,114 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Hepatitis C virus
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- DEY
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- DEY · (2R)-2-({3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothia diazin-7-yl}oxy)propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.81 | 0.82 | 77 | DEY |
| 2 | 1142 | 0.80 | 0.81 | 79 | DEY |
| 3 | 1026 | 0.75 | 0.78 | 102 | empty |
| 4 | 281 | 0.66 | 0.82 | 38 | empty |
| 5 | 99 | 0.49 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3BR9 · Crystal structure of HCV NS5B polymerase with a novel pyridazinone 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 P26663
- Elsewhere: RCSB PDB 3BR9 · PDBe 3BR9 · UniProt P26663
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