GtoPdb database release 2016.4

We are pleased to announce our fourth database release of 2016. Version 2016.4 was published on 13th October 2016. The database is available through the Guide to Pharmacology website, download pages and web-services.

Target updates:

Website updates

A new dendrogram visualisation of VGICs is included on the ion channel page (http://www.guidetopharmacology.org/GRAC/ReceptorFamiliesForward?type=IC). It shows a representation of the amino acid sequence relations of the minimal pore regions of the voltage-gated ion channel superfamily. the visualisation was taken from:

The VGL-Chanome: A Protein Superfamily Specialized for Electrical Signaling and Ionic Homeostasis. Frank H. Yu and William A. Catterall. Sci STKE. 2004 Oct 5;2004(253):re15. PMID: 15467096. DOI: 10.1126/stke.2532004re15

Synpharm

We have created a new sister database to the main Guide to PHARMACOLOGY – SynPharm, a database of drug-responsive protein sequences. The sequences in SynPharm are derived from interactions from the Guide to PHARMACOLOGY and using data from the Protein Data Bank. It is expected that the SynPharm database will grow as the principle Guide to PHARMACOLOGY database is updated – or indeed as further structural data is added to the PDB database pertaining to interactions already documented.

Please read the introductory SynPharm blog post (4th October 2016).

A summary of the current data can be found at synpharm.guidetopharmacology.org/about/data.

Database Statistics

In total the database now contains 14,701 curated interactions across 2,794 human targets and 8,674 ligands. More specifically, the database contain 1,429 human targets that have quantitative interactions to a ligand.

human_targets_pie

Number of human targets in GtoPdb 2016.4. Measured by number of distinct UniProt entries includes for a given target class

ligand_bars

Breakdown of ligand classes in GtoPdb 2016.4

PubChem Links

We refresh our PubChem Substance (SID) submissions at every release and this takes a week or so to surface in their system.  For 2016.4 our  SIDs increased  from 8612 to 8675  (if you want to execute the same query use “IUPHAR/BPS Guide to PHARMACOLOGY”[SourceName]).  The same query at the Compound Identifier (CID) level increases from 6519 to 6565.  As previously  mentioned the 2,110 SIDs that do not merge into CIDs are antibodies, small proteins and large peptides.  Note we have a slight shortfall in the CID numbers you  will find listed in our ligand download lists.  This is because for novel compounds where we were the first submitters to PubChem we now have to catch up with adding the new CIDs into our records.

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Posted in Database updates

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