Research workbench
I. novel HCV NS5B polymerase inhibitors: discovery of indole 2- carboxylic acids with C3-heterocycles
Analyse I. novel HCV NS5B polymerase inhibitors: discovery of indole 2- carboxylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SKH
- Type
- protein
- Length
- 1,116 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS5B RNA_DEPENDENT RNA polymerase
- EC
- 2.7.7.48
- UniProt
- O92972
- Ligands
- 058
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HCV NS5B RNA_DEPENDENT RNA polymerase (EC 2.7.7.48) | protein | 558 | 49% helix, 15% strand | O92972 |
Ligands and binding sites
- 058 · 1-benzyl-5-chloro-3-(2-fluorophenyl)-1H-indole-2-carboxylic acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.81 | 0.82 | 92 | 058 |
| 2 | 1109 | 0.80 | 0.81 | 89 | 058 |
| 3 | 100 | 0.50 | 0.82 | 19 | empty |
| 4 | 92 | 0.49 | 0.82 | 17 | empty |
| 5 | 120 | 0.45 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3SKH · I. Novel HCV NS5B Polymerase Inhibitors: Discovery of Indole 2- Carboxylic Acids 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 O92972
- Elsewhere: RCSB PDB 3SKH · PDBe 3SKH · UniProt O92972
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