Research workbench

X-ray structure of SARS-cov-2 main protease covalently modified by compound grl-091-20

Analyse X-ray structure of SARS-cov-2 main protease covalently modified by compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RC0
Type: protein
Length: 305 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: 4I9, NA
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	305	25% helix, 29% strand	P0DTD1

Ligands and binding sites

4I9 · 5-chloro-4-methylpyridin-3-yl 1H-indole-4-carboxylate · ligand · chains A
NA · Sodium ion · metal · 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	213	0.52	0.77	31	4I9
2	58	0.34	0.77	16	empty
3	53	0.29	0.75	12	empty

Modifications

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

Compared structures

7RC0 · X-ray Structure of SARS-CoV-2 main protease covalently modified by compound GRL-091-20 · 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 7RC0 · PDBe 7RC0 · UniProt P0DTD1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.