Research workbench
Crystal structure of HCV NS5B RNA polymerase with a novel piperazine inhibitor
Analyse Crystal structure of HCV NS5B RNA polymerase with a novel piperazine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQS
- Type
- protein
- Length
- 2,219 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- UniProt
- D0PY27
- Ligands
- JT1, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA-directed RNA polymerase | protein | 553 | 50% helix, 15% strand | D0PY27 |
| B | RNA-directed RNA polymerase | protein | 557 | 50% helix, 16% strand | D0PY27 |
| C | RNA-directed RNA polymerase | protein | 556 | 50% helix, 15% strand | D0PY27 |
Ligands and binding sites
- JT1 · (2R)-4-(5-cyclopropyl[1,3]thiazolo[4,5-d]pyrimidin-2-yl)-N-[3-fluoro-4-(trifluoromethoxy)benzyl]-1-{[4-(trifluoromethyl)phenyl]sulfonyl}piperazine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.84 | 0.85 | 93 | JT1, CL |
| 2 | 890 | 0.83 | 0.84 | 98 | JT1 |
| 3 | 849 | 0.82 | 0.84 | 88 | JT1 |
| 4 | 643 | 0.81 | 0.85 | 75 | JT1 |
| 5 | 947 | 0.75 | 0.78 | 69 | empty |
Interfaces
4 interfaces between chains.
- A–C · 536 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 144 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3VQS · Crystal structure of HCV NS5B RNA polymerase with a novel piperazine inhibitor · the same entry in another collection · chain D against D, 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 D0PY27
- Elsewhere: RCSB PDB 3VQS · PDBe 3VQS · UniProt D0PY27
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