Research workbench
Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221
Analyse Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8T
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- NOL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.05 · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- NOL · N-[(benzyloxy)carbonyl]-O-(tert-butyl)-L-threonyl-3-cyclohexyl-N-[(1S)-2-hydroxy-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}ethyl]-L-alaninamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.51 | 0.78 | 27 | NOL |
| 2 | 97 | 0.36 | 0.75 | 22 | empty |
| 3 | 55 | 0.31 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7C8T · Complex structure of SARS-cov-2 3CL protease with tg-0205221 · 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 7C8T · PDBe 7C8T · UniProt P0DTD1
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