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X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed anti-viral inhibitors

Analyse X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ALV
Type: protein
Length: 302 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicase polyprotein 1AB
EC: 3.4.22.-
UniProt: P59641
Ligands: CY6
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Replicase polyprotein 1AB (EC 3.4.22.-)	protein	302	25% helix, 28% strand	P59641

Ligands and binding sites

CY6 · N-((3S,6R)-6-((S,E)-4-ethoxycarbonyl-1-((S)-2-oxopyrrolidin-3-yl)but-3-en-2-ylcarbamoyl)-2,9-dimethyl-4-oxodec-8-en-3-yl)-5-methylisoxazole-3-carboxamide · 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	191	0.49	0.76	30	CY6

Modifications

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

Compared structures

2ALV · X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed… · 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 P59641
Elsewhere: RCSB PDB 2ALV · PDBe 2ALV · UniProt P59641

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