Research workbench
HCV NS3-4A protease domain with ketoamide inhibitor narlaprevir
Analyse HCV NS3-4A protease domain with ketoamide inhibitor narlaprevir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LON
- Type
- protein
- Length
- 370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Kk-NS4A(21-39)-kk
- UniProt
- Q9ELS8
- Ligands
- NNA, ZN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 181 | 14% helix, 45% strand | Q9ELS8 |
| B | Kk-NS4A(21-39)-kk | protein | 22 | 0% helix, 45% strand | — |
| C | Genome polyprotein | protein | 151 | 10% helix, 51% strand | Q9ELS8 |
| D | Kk-NS4A(21-39)-kk | protein | 16 | 0% helix, 56% strand | — |
Ligands and binding sites
- NNA · (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl) methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · 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 | 103 | 0.61 | 0.87 | 26 | empty |
| 2 | 54 | 0.38 | 0.80 | 14 | empty |
| 3 | 80 | 0.35 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1323 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 291 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 227 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 3LON · HCV NS3-4a protease domain with ketoamide inhibitor narlaprevir · 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 3LON · PDBe 3LON · UniProt Q9ELS8
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