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Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 8

Analyse Crystal structure of SARS-cov-2 main protease (NSP5) in complex with compound 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B77
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase NSP5
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: T0W
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase NSP5 (EC 3.4.22.69)	protein	305	26% helix, 29% strand	P0DTD1

Ligands and binding sites

T0W · 2-(benzotriazol-1-yl)-~{N}-ethyl-~{N}-(furan-3-ylmethyl)ethanamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 6 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	178	0.55	0.80	26	T0W
2	58	0.50	0.86	16	DMS
3	134	0.41	0.75	28	empty

Compared structures

7B77 · Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 8 · the same entry in another collection · chain A against A, TM-score 1.00

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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 7B77 · PDBe 7B77 · UniProt P0DTD1

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