Research workbench
Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1A complex with N-[(2S)-butan-2-yl]-6-[(3R)-3- {[4-(TRIFLUOROMETHOXY)BENZYL]CARBAMOYL}-4-{[4-(trifluoromethoxy) PHENYL]SULFONYL}PIPERAZIN-1-YL]PYRIDAZINE-3-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
- 3QGI
- Type
- protein
- Length
- 561 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- B1PBP5
- Ligands
- 33F
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 561 | 50% helix, 16% strand | B1PBP5 |
Ligands and binding sites
- 33F · N-[(2S)-butan-2-yl]-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide · ligand · chains A
- GOL · Glycerol · additive · 14 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.84 | 0.85 | 96 | 33F, GOL |
| 2 | 62 | 0.44 | 0.83 | 15 | GOL |
| 3 | 134 | 0.42 | 0.75 | 27 | empty |
| 4 | 77 | 0.39 | 0.78 | 20 | empty |
| 5 | 79 | 0.34 | 0.75 | 16 | GOL |
Compared structures
- 3QGI · Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a… · 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 B1PBP5
- Elsewhere: RCSB PDB 3QGI · PDBe 3QGI · UniProt B1PBP5
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