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SARS-cov-2 main protease (mpro) in complex with rupintrivir (P21212)

Analyse SARS-cov-2 main protease (mpro) in complex with rupintrivir (P21212) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L8J
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: AG7
Pockets: 2 · best druggability 0.57

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

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 · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.57	0.77	34	AG7
2	134	0.40	0.74	23	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7L8J · SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212) · 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 7L8J · PDBe 7L8J · UniProt P0DTD1

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