Research workbench
Synthesis of novel 4,5-dihydrofurano indoles and their evaluation as HCV NS5B polymerase inhibitors
Analyse Synthesis of novel 4,5-dihydrofurano indoles and their evaluation as HCV NS5B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UPI
- 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
- 0C2, PO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 47% helix, 15% strand | O92972 |
Ligands and binding sites
- 0C2 · (3S)-6-(2,5-difluorobenzyl)-3-methyl-N-(methylsulfonyl)-8-(2-oxo-1,2-dihydropyridin-3-yl)-3,6-dihydro-2H-furo[2,3-e]indole-7-carboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.81 | 0.82 | 95 | 0C2 |
| 2 | 1154 | 0.81 | 0.82 | 90 | 0C2 |
| 3 | 152 | 0.51 | 0.79 | 25 | empty |
| 4 | 112 | 0.51 | 0.81 | 20 | empty |
| 5 | 115 | 0.45 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3UPI · Synthesis of novel 4,5-dihydrofurano indoles and their evaluation as 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 O92972
- Elsewhere: RCSB PDB 3UPI · PDBe 3UPI · UniProt O92972
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