MolNFT v1 · #116529 · protein

1.0A resolution structure of norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (20-mer) inhibitor

5DGJ · 3C-like protease: “1.0A resolution structure of norovirus 3CL protease in complex an oxadiazole-based, cell permeable…”. X-ray diffraction, 1 ligand (V64), 1 pocket (best druggability 0.47). MolNFT v1 #116529 on GenesisL1: 3D…

PDB: 5DGJ
Type: protein
Length: 168 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like protease
EC: 3.4.22.66
UniProt: Q83883
Ligands: V64
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like protease (EC 3.4.22.66)	protein	168	8% helix, 52% strand	Q83883

Ligands and binding sites

V64 · tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-22-oxa-6,9,14,20,21-pentaazabicyclo[17.2.1]docosa-1(21),19-dien-4-yl]carbamate · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.47	0.78	25	empty

Modifications

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

Compared structures

5DGJ · 1.0A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell… · 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 Q83883
Elsewhere: RCSB PDB 5DGJ · PDBe 5DGJ · UniProt Q83883

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