MolNFT v1 · #40220 · protein
Isothiazoles as active-site inhibitors of HCV NS5B polymerase
2IJN · RNA polymerase NS5B: “Isothiazoles as active-site inhibitors of HCV NS5B polymerase”. X-ray diffraction, 1 ligand (221), 16 pockets (best druggability 0.80). MolNFT v1 #40220 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2IJN
- Type
- protein
- Length
- 1,120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase NS5B
- EC
- 2.7.7.48
- UniProt
- Q99AU2
- Ligands
- 221
- Pockets
- 16 · 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 polymerase NS5B (EC 2.7.7.48) | protein | 559 | 49% helix, 15% strand | Q99AU2 |
| B | RNA polymerase NS5B (EC 2.7.7.48) | protein | 561 | 48% helix, 15% strand | Q99AU2 |
Ligands and binding sites
- 221 · (2R,3R)-3-{[3,5-bis(trifluoromethyl)phenyl]amino}-2-cyano-3-thioxopropanamide · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.80 | 0.81 | 80 | 221 |
| 2 | 990 | 0.79 | 0.81 | 74 | 221 |
| 3 | 1110 | 0.76 | 0.78 | 70 | empty |
| 4 | 118 | 0.52 | 0.81 | 17 | empty |
| 5 | 121 | 0.50 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 550 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2IJN · Isothiazoles as active-site inhibitors of HCV NS5B polymerase · 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 Q99AU2
- Elsewhere: RCSB PDB 2IJN · PDBe 2IJN · UniProt Q99AU2
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