MolNFT v1 · #188400 · protein
Structure of SARS-cov-2 3CL protease in complex with the cyclopropane based inhibitor 1C
7TQ2 · 3C-like proteinase: “Structure of SARS-cov-2 3CL protease in complex with the cyclopropane based inhibitor 1C”. X-ray diffraction, 1 ligand (ISG), 5 pockets (best druggability 0.77). MolNFT v1 #188400 on GenesisL1: 3D structure…
- PDB
- 7TQ2
- Type
- protein
- Length
- 596 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
- ISG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 295 | 27% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- ISG · N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-phenylcyclopropyl]methoxy}carbonyl)-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.77 | 0.80 | 75 | empty |
| 2 | 190 | 0.57 | 0.80 | 36 | empty |
| 3 | 209 | 0.54 | 0.78 | 22 | ISG |
| 4 | 191 | 0.52 | 0.78 | 30 | ISG |
| 5 | 52 | 0.30 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1110 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7TQ2 · Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 1c · 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 7TQ2 · PDBe 7TQ2 · UniProt P0DTD1
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