Dockable metabolites libraries

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sure, of course, except KEGG contains a lot of things that are not metabolites. But sure, 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:

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.