Research workbench
The crystal structure of COVID-19 main protease in complex with an inhibitor shikonin
Analyse The crystal structure of COVID-19 main 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
- 7CA8
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- FNO
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 296 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 273 | 24% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- FNO · 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.72 | 0.77 | 63 | empty |
| 2 | 411 | 0.63 | 0.77 | 56 | empty |
| 3 | 322 | 0.58 | 0.76 | 42 | empty |
| 4 | 238 | 0.47 | 0.73 | 46 | empty |
| 5 | 112 | 0.40 | 0.76 | 25 | FNO |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7CA8 · The crystal structure of COVID-19 main 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 P0DTD1
- Elsewhere: RCSB PDB 7CA8 · PDBe 7CA8 · UniProt P0DTD1
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