MolNFT v1 · #172800 · protein
Structure of SARS-cov-2 main protease bound to 2,4'- dimethylpropiophenone.
7ADW · 3C-like proteinase: “Structure of SARS-cov-2 main protease bound to 2,4'- dimethylpropiophenone.”. X-ray diffraction, 2 ligands (R7Q, CL), 4 pockets (best druggability 0.54). MolNFT v1 #172800 on GenesisL1: 3D structure, binding…
- PDB
- 7ADW
- 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
- R7Q, CL
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- R7Q · 2-methyl-1-(4-methylphenyl)propan-1-one · ligand · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- IMD · Imidazole · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.54 | 0.88 | 18 | DMS |
| 2 | 192 | 0.48 | 0.76 | 26 | R7Q |
| 3 | 84 | 0.37 | 0.76 | 16 | empty |
| 4 | 72 | 0.31 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7ADW · Structure of SARS-CoV-2 Main Protease bound to 2,4'-Dimethylpropiophe . · 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 7ADW · PDBe 7ADW · UniProt P0DTD1
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