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Structure of SARS-cov-2 3CL protease in complex with the cyclopropane based inhibitor 10D
Analyse Structure of SARS-cov-2 3CL protease in complex with the cyclopropane based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TQ5
- Type
- protein
- Length
- 597 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
- P0DTD1
- Ligands
- IRW, ITX, CL
- Pockets
- 7 · best druggability 0.72
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 | 26% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- IRW · (1S,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl) cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- ITX · (1R,2S)-1-hydroxy-2-{[N-({[(1R,2R)-2-(4-methoxyphenyl) cyclopropyl]methoxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.72 | 0.76 | 72 | empty |
| 2 | 111 | 0.52 | 0.82 | 19 | empty |
| 3 | 187 | 0.52 | 0.78 | 26 | IRW, ITX |
| 4 | 204 | 0.51 | 0.77 | 27 | IRW, ITX |
| 5 | 106 | 0.40 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7TQ5 · Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 10d · 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 7TQ5 · PDBe 7TQ5 · UniProt P0DTD1
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