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Crystal structure of SARS-cov-2 main protease (3CLPRO/MPRO) covalently bound to compound C7

Analyse Crystal structure of SARS-cov-2 main protease (3CLPRO/MPRO) covalently bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MLF
Type: protein
Length: 304 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: C7A
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	304	25% helix, 27% strand	P0DTD1

Ligands and binding sites

C7A · N-(4-tert-butylphenyl)-2-chloro-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl) ethyl]acetamide · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	259	0.56	0.78	27	C7A
2	245	0.51	0.75	31	empty

Modifications

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

Compared structures

7MLF · Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 7MLF · PDBe 7MLF · UniProt P0DTD1

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