Research workbench
HCV NS3 protease domain with P1-P3 macrocyclic ketoamide inhibitor
Analyse HCV NS3 protease domain with P1-P3 macrocyclic ketoamide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNX
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV NS3 protease; HCV NS4A peptide
- UniProt
- Q9ELS8
- Ligands
- JZT, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV NS3 protease | protein | 181 | 15% helix, 45% strand | Q9ELS8 |
| B | HCV NS4A peptide | protein | 22 | 0% helix, 50% strand | Q9ELS8 |
| C | HCV NS3 protease | protein | 151 | 10% helix, 50% strand | Q9ELS8 |
| D | HCV NS4A peptide | protein | 16 | 0% helix, 56% strand | Q9ELS8 |
Ligands and binding sites
- JZT · (2R)-2-{(3S,13S,16aS,17aR,17bS)-13-[({(1S)-1-[(4,4-dimethyl-2,6-dioxopiperidin-1-yl)methyl]-2,2-dimethylpropyl}carbamoyl)amino]-17,17-dimethyl-1,14-dioxooctadecahydro-2H-cyclopropa[3,4]pyrrolo[1,2-a][1,4]diazacyclohexadecin-3-yl}-2-hydroxy-N-prop-2-en-1-ylethanamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.59 | 0.84 | 29 | empty |
| 2 | 57 | 0.39 | 0.80 | 16 | empty |
| 3 | 94 | 0.36 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1280 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 848 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 300 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 210 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 3KNX · HCV NS3 protease domain with P1-P3 macrocyclic ketoamide inhibitor · 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 Q9ELS8
- Elsewhere: RCSB PDB 3KNX · PDBe 3KNX · UniProt Q9ELS8
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