Research workbench
HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021
Analyse HCV NS3-4A protease domain complexed with a 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
- 2GVF
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- Ligands
- NHN, ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein | protein | 183 | 15% helix, 45% strand | — |
| B | Polyprotein | protein | 22 | 0% helix, 45% strand | — |
| C | Polyprotein | protein | 152 | 12% helix, 50% strand | — |
| D | Polyprotein | protein | 16 | 0% helix, 56% strand | — |
Ligands and binding sites
- NHN · (6R,8S,11S)-11-cyclohexyl-N-(1-{[(2-{[(1S)-2-(dimethylamino)-2-oxo-1-phenylethyl]amino}-2-oxoethyl)amino](oxo)acetyl}butyl)-10,13-dioxo-2,5-dioxa-9,12-diazatricyclo[14.3.1.1~6,9~]henicosa-1(20),16,18-triene-8-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.59 | 0.85 | 26 | empty |
| 2 | 57 | 0.37 | 0.79 | 15 | empty |
| 3 | 58 | 0.31 | 0.75 | 16 | empty |
| 4 | 63 | 0.28 | 0.73 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1307 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 869 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 326 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2GVF · HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021 · 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
- Elsewhere: RCSB PDB 2GVF · PDBe 2GVF
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