MolNFT v1 · #65738 · protein
Hepatitis C virus polymerase NS5B with saccharin inhibitor
3H5S · RNA-directed RNA polymerase: “Hepatitis C virus polymerase NS5B with saccharin inhibitor”. X-ray diffraction, 1 ligand (H5S), 12 pockets (best druggability 0.80). MolNFT v1 #65738 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3H5S
- 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
- H5S
- Pockets
- 12 · 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 | 557 | 49% helix, 15% strand | P26663 |
Ligands and binding sites
- H5S · (5S)-5-tert-butyl-1-(4-fluoro-3-methylbenzyl)-4-hydroxy-3-[8-(methylsulfonyl)-1,1-dioxido-6,7,8,9-tetrahydroisothiazolo[4,5-h]isoquinolin-3-yl]-1,5-dihydro-2H-pyrrol-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.80 | 0.82 | 80 | H5S |
| 2 | 1087 | 0.80 | 0.81 | 84 | H5S |
| 3 | 902 | 0.74 | 0.78 | 88 | empty |
| 4 | 325 | 0.66 | 0.81 | 39 | empty |
| 5 | 70 | 0.47 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3H5S · Hepatitis C virus polymerase NS5B with saccharin 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 3H5S · PDBe 3H5S · UniProt P26663
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