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

http://zinc15.docking.org/catalogs/subsets/metabolite/

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

http://zinc15.docking.org/catalogs/subsets/biogenic/

http://zinc.docking.org/subsets/zmd

these are the ZINC 12 metabolites. The download links are on the page. For instance to download mol2 format, you would use: http://zinc.docking.org/db/special/97/usual.sdf.csh

For ZINC15, the answer depends on three questions: a. purchasable vs all b. endogenous human vs all c. format (sdf, mol2, db.gz, db2.gz, pdbqt) d. assuming near pH 6-8 but if low pH or high pH must specify

The syntax will get much clearer soon. for now: For instance, all endogenous human metabolites:

zinc15.docking.org/protomers.mol2.gz?catalog.np=3

all endogenous human metabolites you can buy

http://zinc15.docking.org/protomers.mol2.gz?catalog.np=3&substance.purchasability=for-sale&count=all

Good enough? Lots more options...