Research workbench
HCV NS5B in complex with IDX375
Analyse HCV NS5B in complex with IDX375 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EAW
- Type
- protein
- Length
- 1,118 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
- 0NQ, SO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 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 | 559 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- 0NQ · N-{(1S)-3-[(5S)-5-tert-butyl-1-(3,3-dimethylbutyl)-4-hydroxy-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]-1-ethoxy-1-oxido-1,4-dihydro-2,4,1-benzodiazaphosphinin-7-yl}methanesulfonamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.80 | 0.81 | 92 | 0NQ, SO4, PEG |
| 2 | 991 | 0.80 | 0.81 | 78 | 0NQ, SO4 |
| 3 | 633 | 0.70 | 0.78 | 56 | empty |
| 4 | 137 | 0.48 | 0.78 | 19 | empty |
| 5 | 132 | 0.46 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 299 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EAW · HCV NS5B in complex with IDX375 · the same entry in another collection · chain B against B, 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 4EAW · PDBe 4EAW · UniProt O92972
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