Research workbench
Structure of SARS-cov-2 main protease bound to triglycidyl isocyanurate.
Analyse Structure of SARS-cov-2 main protease bound to triglycidyl isocyanurate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AQJ
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- S7H, RV8
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- S7H · 1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione · ligand · chains A
- RV8 · Triglycidyl isocyanurate · 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 | 247 | 0.57 | 0.78 | 28 | S7H, RV8 |
| 2 | 66 | 0.32 | 0.75 | 16 | empty |
| 3 | 69 | 0.31 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7AQJ · Structure of SARS-CoV-2 Main Protease bound to Triglycidyl isocyanurate. · 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 7AQJ · PDBe 7AQJ · UniProt P0DTD1
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