MolNFT v1 · #190900 · protein
SARS-cov-2 main protease (mpro) covalently modified with a penicillin derivative
7Z59 · 3C-like proteinase NSP5: “SARS-cov-2 main protease (mpro) covalently modified with a penicillin derivative”. X-ray diffraction, 1 ligand (IFO), 4 pockets (best druggability 0.48). MolNFT v1 #190900 on GenesisL1: 3D structure…
- PDB
- 7Z59
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- IFO
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- IFO · (3S)-4-[[2,4-bis(fluoranyl)phenyl]methoxy]-2-methyl-4-oxidanylidene-3-[[(Z)-3-oxidanylidene-2-(2-phenoxyethanoylamino)prop-1-enyl]amino]butane-2-sulfinic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.48 | 0.79 | 22 | IFO |
| 2 | 58 | 0.47 | 0.85 | 18 | EDO |
| 3 | 59 | 0.34 | 0.77 | 16 | empty |
| 4 | 80 | 0.31 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7Z59 · SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative · 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 7Z59 · PDBe 7Z59 · UniProt P0DTD1
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