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Structure of the SARS-cov-2 main protease in complex with inhibitor MPI21

Analyse Structure of the SARS-cov-2 main protease in complex with inhibitor MPI21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RVU
Type: protein
Length: 303 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
UniProt: P0DTD1
Ligands: 7XT
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase	protein	303	24% helix, 27% strand	P0DTD1

Ligands and binding sites

7XT · N-[(benzyloxy)carbonyl]-3-methyl-L-isovalyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.49	0.77	32	empty
2	169	0.48	0.76	28	7XT

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7RVU · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI21 · 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 7RVU · PDBe 7RVU · UniProt P0DTD1

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