Metabolites

Many people are interested in metabolites, including purchasable metabolites. We get emails such as this one:

We are looking into HMDB  for GPCR deorphanization tasks, 
and for practical purposes want to focus on purchasable molecules only.
I was wondering if it is possible to download a purchasable subset of
HMDB (such that each molecule is purchasable (but without molecules
that are metabolites of purchasable ones, but not purchasable on there own)

We begin by doing the best we can on the question as asked, and then broaden the question:

To get the purchasable compounds in HMDB, you would use:

http://zinc15.docking.org/catalogs/hmdb/substances/subsets/purchasable

To download these in SMILES, you would just add .smi to the end, and say you want all of them, thus:

http://zinc15.docking.org/catalogs/hmdb/substances/subsets/purchasable.smi?count=all

Unfortunately, we do not keep track of which compounds are metabolites of other molecules. If you have access to such a mapping, let us know and we can help you do the filtering you request.

Turning to the questions more broadly raised in the email, we image our correspondent is using "HMDB" as a proxy for "human metabolites". This is not actually correct. HMDB is a very powerful resource that also includes drug metabolites, plant and food metabolites, and other xenobiotics. Fortunately, HMDB does break these different classes out, and we have categorized them separately in ZINC.

Thus, to access only endogenous human metabolites from HMDB in ZINC, use:

http://zinc15.docking.org/catalogs/hmdbendo/substances/subsets/purchasable

But we wonder whether our reader was actually really interested in endogenous human metabolites, not only in HMDB but from any other public sources. If so, we suggest using the ZINC endogenous subset, thus:

http://zinc15.docking.org/substances/subsets/endogenous+purchasable

To get a thousand of these in SDF form, just do:

http://zinc15.docking.org/substances/subsets/endogenous+purchasable.sdf?count=100

Now, you may be wondering, which catalogs contribute to the endogenous subset of ZINC. For this, you would use:

 http://zinc15.docking.org/catalots/subsets/endogenous

If you believe a catalog has been incorrectly curated, please write us!