MolNFT v1 · #36577 · protein
HCV NS3 protease domain with NS4A peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines
2F9V · NS3 PROTEASE/HELICASE: “HCV NS3 protease domain with NS4A peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines”. X-ray diffraction, 2 ligands (BN6, ZN), 2 pockets (best druggability 0.60). MolNFT v1 #36577 on…
- PDB
- 2F9V
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 PROTEASE/HELICASE; Polyprotein
- Ligands
- BN6, ZN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3 PROTEASE/HELICASE | protein | 183 | 15% helix, 45% strand | — |
| B | Polyprotein | protein | 22 | 0% helix, 45% strand | — |
| C | NS3 PROTEASE/HELICASE | protein | 152 | 10% helix, 51% strand | — |
| D | Polyprotein | protein | 16 | 0% helix, 56% strand | — |
Ligands and binding sites
- BN6 · (2S,8R,9S,15S)-15-cyclohexyl-9,12-bis(cyclopropylmethyl)-8-hydroxy-20-methyl-4,7,11,14,17-pentaoxo-2-phenyl-18-oxa-3,6,10,12,13,16-hexaazahenicosan-1-oic acid · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.60 | 0.85 | 26 | empty |
| 2 | 58 | 0.37 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1293 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 855 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 310 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2F9V · HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2… · 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 2F9V · PDBe 2F9V
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