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Joint X-RAY/NEUTRON structure of SARS-cov-2 main protease (mpro) in complex with MCULE5948770040

Analyse Joint X-RAY/NEUTRON structure of SARS-cov-2 main protease (mpro) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N8C
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction; neutron diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: YD1
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction; neutron diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	306	24% helix, 28% strand	P0DTD1

Ligands and binding sites

YD1 · 6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione · 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	196	0.51	0.77	30	YD1
2	214	0.51	0.76	32	empty

Compared structures

7N8C · Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with… · 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 7N8C · PDBe 7N8C · UniProt P0DTD1

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