Research workbench
The crystal structure of SARS-cov-2 3CL protease in complex with compound 1
Analyse The crystal structure of SARS-cov-2 3CL protease in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VTH
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- 7XB
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 298 | 27% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- 7XB · 2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide · ligand · 2 copies · chains A, B
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 | 931 | 0.75 | 0.78 | 75 | empty |
| 2 | 239 | 0.56 | 0.78 | 37 | empty |
| 3 | 153 | 0.54 | 0.80 | 27 | empty |
| 4 | 157 | 0.47 | 0.77 | 26 | 7XB |
| 5 | 152 | 0.46 | 0.76 | 28 | 7XB |
Interfaces
1 interface between chains.
- A–B · 1235 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7VTH · The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1 · 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 P0DTC1
- Elsewhere: RCSB PDB 7VTH · PDBe 7VTH · UniProt P0DTC1
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