MolNFT v1 · #189781 · protein
SARS-cov-2 3CL protease (3CLPRO) in complex with a covalent inhibitor
7VVT · 3C-like proteinase: “SARS-cov-2 3CL protease (3CLPRO) in complex with a covalent inhibitor”. X-ray diffraction, 1 ligand (80X), 7 pockets (best druggability 0.76). MolNFT v1 #189781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7VVT
- Type
- protein
- Length
- 586 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
- P0DTC1
- Ligands
- 80X
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 25% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 286 | 26% helix, 31% strand | P0DTC1 |
Ligands and binding sites
- 80X · N-(3-chlorophenyl)-2-[(2R)-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanamide · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.76 | 0.78 | 108 | empty |
| 2 | 55 | 0.56 | 0.89 | 16 | empty |
| 3 | 95 | 0.53 | 0.84 | 24 | empty |
| 4 | 180 | 0.50 | 0.77 | 29 | 80X |
| 5 | 134 | 0.49 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1259 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7VVT · SARS-CoV-2 3CL protease (3CLpro) in complex with a covalent 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 P0DTC1
- Elsewhere: RCSB PDB 7VVT · PDBe 7VVT · UniProt P0DTC1
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