Research workbench
Crystal structure of hepatitis C virus RNA-dependent RNA polymerase NS5B in complex with optimized small molecule fragments
Analyse Crystal structure of hepatitis C virus RNA-dependent RNA polymerase NS5B in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CJ5
- Type
- protein
- Length
- 1,125 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
- SX6
- Pockets
- 14 · 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 | 562 | 48% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 563 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- SX6 · N-(4-bromo-2-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]carbonyl}phenyl)-4-morpholin-4-yl-4-oxobutanamide · 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 | 1169 | 0.80 | 0.81 | 79 | empty |
| 2 | 1144 | 0.79 | 0.81 | 82 | empty |
| 3 | 840 | 0.74 | 0.78 | 85 | empty |
| 4 | 248 | 0.66 | 0.83 | 30 | empty |
| 5 | 119 | 0.49 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 711 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3CJ5 · Crystal structure of hepatitis c virus rna-dependent rna polymerase ns5b in complex with… · 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 3CJ5 · PDBe 3CJ5 · UniProt P26663
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