Research workbench
Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7- dihydro-5H-INDOLO[1,2-D][1,4]BENZODIAZEPIN-10-yl) CARBONYL]AMINO}CYCLOPENTYL)CARBONYL]AMINO}PHENYL)PROP-2-enoic acid and (2R)-4-(6-chloropyridazin-3-yl)-N-(4-methoxybenzyl)-1-{[4- (TRIFLUOROMETHOXY)PHENYL]SULFONYL}PIPERAZINE-2-carboxamide
Analyse Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QGF
- Type
- protein
- Length
- 1,067 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
- Q9WMX2
- Ligands
- 23E, 46F, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 534 | 49% helix, 16% strand | Q9WMX2 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 533 | 48% helix, 16% strand | Q9WMX2 |
Ligands and binding sites
- 23E · (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
- 46F · (2R)-4-(6-chloropyridazin-3-yl)-N-(4-methoxybenzyl)-1-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.82 | 0.83 | 94 | 46F |
| 2 | 1087 | 0.81 | 0.82 | 84 | 46F, SO4 |
| 3 | 105 | 0.47 | 0.80 | 24 | empty |
| 4 | 109 | 0.46 | 0.79 | 22 | empty |
| 5 | 103 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1045 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3QGF · Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex 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 Q9WMX2
- Elsewhere: RCSB PDB 3QGF · PDBe 3QGF · UniProt Q9WMX2
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