MolNFT v1 · #180703 · protein
SARS-cov-2 main protease (mpro) in complex with rupintrivir (P21)
7L8I · 3C-like proteinase: “SARS-cov-2 main protease (mpro) in complex with rupintrivir (P21)”. X-ray diffraction, 1 ligand (AG7), 7 pockets (best druggability 0.76). MolNFT v1 #180703 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7L8I
- Type
- protein
- Length
- 610 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
- AG7
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- AG7 · 4-{2-(4-fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo-heptanoylamino}-5-(2-oxo-pyrrolidin-3-yl)-pentanoic acid ethyl ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.76 | 0.79 | 82 | empty |
| 2 | 218 | 0.51 | 0.76 | 26 | AG7 |
| 3 | 216 | 0.50 | 0.76 | 30 | AG7 |
| 4 | 106 | 0.36 | 0.74 | 25 | empty |
| 5 | 77 | 0.33 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1615 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7L8I · SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21) · 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 7L8I · PDBe 7L8I · UniProt P0DTD1
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