MolNFT v1 · #80498 · protein
Sar development and discovery of potent indole-based inhibitors of the hepatitis C virus NS5B polymerase
3TYQ · RNA-directed RNA polymerase: “Sar development and discovery of potent indole-based inhibitors of the hepatitis C virus NS5B polymerase”. X-ray diffraction, 2 ligands (HI4, PO4), 16 pockets (best druggability 0.80). MolNFT v1 #80498…
- PDB
- 3TYQ
- Type
- protein
- Length
- 1,121 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
- HI4, PO4
- Pockets
- 16 · 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 | 563 | 49% helix, 15% strand | O92972 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 558 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- HI4 · 5-ethyl-1-(2-fluoro-5-nitrobenzyl)-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.80 | 0.82 | 91 | HI4 |
| 2 | 1076 | 0.80 | 0.81 | 91 | HI4 |
| 3 | 98 | 0.50 | 0.82 | 19 | empty |
| 4 | 126 | 0.49 | 0.80 | 19 | empty |
| 5 | 117 | 0.44 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3TYQ · SAR development and discovery of potent indole-based inhibitors of the hepatitis c virus… · 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 O92972
- Elsewhere: RCSB PDB 3TYQ · PDBe 3TYQ · UniProt O92972
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