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
- 3D5M
- Type
- protein
- Length
- 1,116 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
- 4MS
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 559 | 48% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 557 | 48% helix, 15% strand | P26663 |
Ligands and binding sites
- 4MS · N-({3-[(5S)-5-tert-butyl-1-(3-chloro-4-fluorobenzyl)-4-hydroxy-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]-1,1-dioxido-1,2-benzis othiazol-7-yl}methyl)methanesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.80 | 0.82 | 84 | 4MS |
| 2 | 1139 | 0.80 | 0.82 | 78 | 4MS |
| 3 | 406 | 0.65 | 0.79 | 44 | empty |
| 4 | 527 | 0.65 | 0.76 | 52 | empty |
| 5 | 122 | 0.50 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3D5M · 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 3D5M · PDBe 3D5M · UniProt P26663
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