Research workbench
Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor
Analyse Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CDE
- Type
- protein
- Length
- 1,114 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
- P26663
- Ligands
- N3H
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 50% helix, 15% strand | P26663 |
Ligands and binding sites
- N3H · N-{3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.80 | 0.81 | 85 | N3H |
| 2 | 1074 | 0.80 | 0.81 | 83 | N3H |
| 3 | 1195 | 0.71 | 0.75 | 92 | empty |
| 4 | 314 | 0.68 | 0.83 | 39 | empty |
| 5 | 97 | 0.50 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3CDE · Crystal structure of HCV NS5B polymerase with a novel Pyridazi 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 3CDE · PDBe 3CDE · UniProt P26663
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