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Structure of SARS-COV2 3CL protease covalently bound to peptidomimetic inhibitor
Analyse Structure of SARS-COV2 3CL protease covalently bound to peptidomimetic inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MBI
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- YWJ, FN7
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 26% helix, 29% strand | P0DTD1 |
| B, D | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 26% helix, 29% strand | P0DTD1 |
| C | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- YWJ · 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-3-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- FN7 · 2,4,6-trimethylpyridine-3-carboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.76 | 0.79 | 86 | empty |
| 2 | 464 | 0.63 | 0.77 | 56 | empty |
| 3 | 253 | 0.57 | 0.78 | 31 | YWJ |
| 4 | 244 | 0.55 | 0.77 | 28 | empty |
| 5 | 197 | 0.52 | 0.78 | 28 | YWJ |
Interfaces
4 interfaces between chains.
- B–C · 1570 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 150 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7MBI · Structure of SARS-CoV2 3CL protease covalently bound to peptidomimetic inhibitor · 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 7MBI · PDBe 7MBI · UniProt P0DTD1
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