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

these are the ZINC 12 metabolites. The download links are on the page. For instance to download mol2 format, you would use:

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:

all endogenous human metabolites you can buy

Good enough? Lots more options...