Glutaconyl-CoA is an intermediate in the metabolism of lysine. It is an organic compound containing a coenzyme substructure, which classifies it as a fatty ester lipid molecule. Being a lipid makes the molecule hydrophobic, which makes it insoluble in water. The molecule has a molecular formula of , and a molecular weight 879.62 grams per mole.
Glutaconyl-CoA is postulated to be the main toxin in glutaric aciduria type 1. In certain fermentative bacteria, glutaconyl-CoA decarboxylation is catalyzed by a Na<sup>+</sup>-dependent decarboxylase () and is coupled with Na<sup>+</sup> ion translocation, which creates a sodium-motive force as an alternate energy source for these organisms.