Research workbench
Crystal structure of hcov-NL63 3C-like protease in complex with an inhibitor shikonin
Analyse Crystal structure of hcov-NL63 3C-like protease in complex with an inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EO7
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6U6
- Ligands
- FNO
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 24% helix, 29% strand | P0C6U6 |
Ligands and binding sites
- FNO · 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.68 | 0.75 | 81 | empty |
| 2 | 513 | 0.66 | 0.77 | 63 | empty |
| 3 | 561 | 0.66 | 0.77 | 66 | empty |
| 4 | 118 | 0.40 | 0.75 | 20 | FNO |
| 5 | 105 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7EO7 · Crystal structure of HCoV-NL63 3C-like protease in complex with an inhibitor Shikonin · 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 P0C6U6
- Elsewhere: RCSB PDB 7EO7 · PDBe 7EO7 · UniProt P0C6U6
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