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Structure of the SARS-cov-2 main protease in complex with inhibitor MPI4

Analyse Structure of the SARS-cov-2 main protease in complex with inhibitor MPI4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JQ1
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: VHJ
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	306	26% helix, 28% strand	P0DTD1

Ligands and binding sites

VHJ · N-[(benzyloxy)carbonyl]-L-valyl-N-{(2S)-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-L-phenylalaninamide · ligand · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.51	0.77	28	VHJ
2	55	0.44	0.83	17	empty
3	78	0.35	0.75	15	empty
4	76	0.33	0.75	17	empty

Modifications

Observed in the structure: 2 modified, 1 covalent (oxidation, covalent ligand).

Compared structures

7JQ1 · Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI4 · 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 7JQ1 · PDBe 7JQ1 · UniProt P0DTD1

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