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Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI12

Analyse Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UUB
Type: protein
Length: 301 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.63
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: 3C-like proteinase nsp5
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: 7VB
Pockets: 2 · best druggability 0.41

Structure

x-ray diffraction · resolution 1.63 · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase nsp5 (EC 3.4.22.69)	protein	301	25% helix, 29% strand	P0DTD1

Ligands and binding sites

7VB · N-[(benzyloxy)carbonyl]-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methylidene-L-norvalinamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 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	136	0.41	0.75	23	7VB
2	119	0.39	0.74	26	empty

Modifications

Observed in the structure: 4 modified, 1 covalent (oxidation, covalent ligand).

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 7UUB · PDBe 7UUB · UniProt P0DTD1

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