Accessing WHO Essential Medicines in GtoPdb

The Guide to Pharmacology (GtoPdb) currently contains data on over 10,000 different ligands which are categorised into an number of different groups or classifications. The ligand list page ( provides a directory of all the ligands described in the database, divided into subsets according to chemical category.

We have recently added a WHO Essential Medicine subset, which contains ligands in GtoPdb that are also in the latest WHO Model List of Essential Medicines (21st list, 2019) ( This totals 224 ligands in our 2020.3 release.

Selecting the WHO tab from the ligand list page shows this subset (Figure 1). Users can also download this set of ligands (as csv file) by clicking on the link in the top-right.

Accessing WHO tagged GtoPdb compound in PubChem

GtoPdb regularly uploads its set of compounds to PubChem, which provides all GtoPdb ligands with PubChem Substance Identifiers (SIDs), which are in turn mapped (by PubChem) to PubChem Compound Identifiers (CIDs). As part of our PubChem upload process we have developed our curatorial tagging within the depositor comment sections in the substance records (SIDs). This means users are able to make domain-specific queries, to be executed from both the PubChem Substance (SID) and PubChem Compound (CID) interfaces, by using an advanced search of ‘comments’ fields.

We have now added a WHO tag to the comments fields in our PubChem upload (see example for cholorquine, Figure 2). chloroquine2

Figure 2. Depositor comment for Chloroquine (PubChem Substance ID 178102177) showing GtoPdb curatorial tagging to mark substance as included in WHO Essential Medicines List.

Therefore it is now possible, through the query below to easily access the WHO Essential Medicines in GtoPdb through PubChem.


Figure 3. Search result in PubChem for IUPHAR/BPS Guide to PHARMACOLOGY substances that include ‘gtopdb_who’ in the comments.


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Posted in Technical, Tutorials and Guides

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