MolNFT v1 · #173358 · protein
Structure of SARS-cov-2 main protease bound to glutathione isopropyl ester
7AX6 · 3C-like proteinase: “Structure of SARS-cov-2 main protease bound to glutathione isopropyl ester”. X-ray diffraction, 1 ligand (S8H), 4 pockets (best druggability 0.53). MolNFT v1 #173358 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7AX6
- Type
- protein
- Length
- 306 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
- S8H
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- S8H · (2~{S})-2-azanyl-5-oxidanylidene-5-[[(2~{S})-1-oxidanylidene-1-[(2-oxidanylidene-2-propan-2-yloxy-ethyl)amino]-3-sulfanyl-propan-2-yl]amino]pentanoic acid · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 2 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 | 73 | 0.53 | 0.86 | 15 | empty |
| 2 | 203 | 0.50 | 0.76 | 25 | IMD |
| 3 | 78 | 0.37 | 0.77 | 18 | empty |
| 4 | 81 | 0.33 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7AX6 · Structure of SARS-CoV-2 Main Protease bound to Glutathione isopropyl ester · 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 7AX6 · PDBe 7AX6 · UniProt P0DTD1
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