MolNFT v1 · #173892 · protein
Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2.
7BE7 · 3C-like proteinase: “Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2.”. X-ray diffraction, 3 ligands (ALD, NA, CL), 8 pockets (best druggability 0.77). MolNFT v1 #173892 on GenesisL1: 3D…
- PDB
- 7BE7
- Type
- protein
- Length
- 607 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
- ALD, NA, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 25% helix, 28% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- ALD · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.77 | 0.79 | 79 | empty |
| 2 | 91 | 0.55 | 0.85 | 28 | EDO |
| 3 | 182 | 0.50 | 0.77 | 30 | ALD |
| 4 | 191 | 0.48 | 0.76 | 29 | ALD |
| 5 | 252 | 0.48 | 0.73 | 44 | PEG, EDO |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7BE7 · Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of… · 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 7BE7 · PDBe 7BE7 · UniProt P0DTD1
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