Dockable metabolites libraries
sure, of course, except KEGG contains a lot of things that are not metabolites. But sure, http://zinc.docking.org/catalogs/keggviapc. If you want to consider individual databases and catalogs, some of which contain some metabolites, then there's also HMDB. Biocyc.
Here is a list of metabolite databases in ZINC 15
Here are the catalogs that contain only endogeous human metabolites as far as we know: http://zinc15.docking.org/catalogs/subsets/endogenous/
here are the ones that contain natural products, many of which are metabolites
It's a big topic, I didn't know exactly what you wanted.