MolNFT v1 · #183110 · protein
Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2 in spacegroup C2.
7NF5 · 3C-like proteinase: “Crystal structure of mg-132 covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2 in spacegroup…”. X-ray diffraction, 3 ligands (ALD, NA, CL), 2 pockets (best druggability 0.52). MolNFT v1 #183110 on…
- PDB
- 7NF5
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- 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
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- ALD · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- IPA · Isopropyl alcohol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.52 | 0.79 | 29 | ALD |
| 2 | 153 | 0.45 | 0.76 | 29 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NF5 · 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 7NF5 · PDBe 7NF5 · UniProt P0DTD1
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