The 5th IUPHAR/BPS Guide to PHARMACOLOGY database release of 2017 includes updates to several target families, and new targets and ligands added, focusing on those relevant to immunopharmacology. We also announce a new organisation for ligand families and groups. This update also includes the beta v2.0 release of the IUPHAR Guide to IMMUNOPHARMACOLOGY portal taking into account early feedback from our beta testers. Eagle-eyed users may have noticed a new homepage layout for GtoPdb, which has been reorganised to highlight important new features at the top of the page, with quick links to the main database pages on the left, and news items and publications below.
Target and ligand updates
- Updates to GPCRs, including Dopamine, Endothelin receptors, Glucagon, Prostanoid and Succinate receptors
- Updates to ion channels, including: Epithelial sodium channels (ENaC) and P2X receptors
- New family Butyrophilin and butyrophilin-like proteins
- Reorganisation and additions to Immune checkpoint proteins, which now has the subfamilies Immune checkpoint catalytic receptors and Other immune checkpoint proteins. There is a also a group of Immune checkpoint modulators under the ligand families list (see below)
We have introduced a new organisation of peptide ligands into families. This can be reached via a link from the “Ligands” submenu of the main navigation menu. This started with the aim of grouping related peptide sequences together into families to aid discoverability and allow us to add comments and references pertaining to the family as a whole. We have also experimented with grouping together some other types of ligands (such as the Immune checkpoint modulators) linked by their mechanism of action (although not a family in the phylogenetic sense). Feedback on this new organisation is welcome.
Ligand activity graphs
Continuing on from previous updates (releases 2017.2 and 2017.4), where we described the addition of graphs to visualise ligand activity data for targets across species using data from GtoPdb and the med-chem database, ChEMBL, we have now extended this feature to all ligands in GtoPdb with quantitative activity data at targets, even where the ligands do not have data in ChEMBL. There will also be cases where the GtoPdb curators just haven’t yet identified the ligand in ChEMBL, in particular peptides can be difficult to search for because of naming differences and lack of standard chemical structure descriptors.
Expanded database cross-links
From time to time we internaly review the databases that we cross-link to and from, to make sure they are current and useful. During an iteration of this process within this release cycle we introduced several new resources that have value for users. These changes are explained in a separate post.
IUPHAR Guide to IMMUNOPHARMACOLOGY beta v2.0
This update also sees the release of the beta v2.0 of the new Guide to IMMUNOPHARMACOLOGY portal. This is a Wellcome Trust-funded extension to the existing database, aiming to improve data exchange between immunology and pharmacology. Read the release notes and technical update here. We are grateful for all the feedback received so far and welcome continued comments and bug reports as we further develop the new data and portal.
Database content and statistics
For the full statistics on release 2017.5 please see the about page on the GtoPdb site. In summary, there are now 15,281 curated binding constants between 2825 targets and 8978 ligands. (N.B. for various reasons, not all those targets and ligands have quantitative binding data; in the third table below the current number of human targets with quantitative data is 1431.)
[…] statistics of content are presented as usual in the release notes and the The Guide to IMMUNOPHARMACOLOGY has a separate update. This post describes changes and […]
[…] (1). Since 2015 we have made nine PubChem submissions for new releases of our database. For 2017.5 (see release notes for version 2017.5) we now have 8978 Substance Identifiers (SIDs) (PubChem query “IUPHAR/BPS Guide to […]