G protein-coupled receptors database

GPCRDB
Content
Description G protein-coupled receptor data, web tools & diagrams
Data types
captured		 Structures, mutants, sequences
Contact
Research center University of Copenhagen
Authors David Gloriam
Primary citation Isberg & al. (2014) [1]
Release date 1993
Access
Website http://www.gpcrdb.org
Miscellaneous
Curation policy Manual and experimental data-derived

GPCRdb contains data, web tools and diagrams for G protein-coupled receptors (GPCRs). It stores a manual annotation of all GPCR crystal structures, the largest collections of receptor mutants and reference sequence alignments. The tools run directly in the web browser allowing for swift analysis of structures, sequence similarities, receptor relationships, homology models, drug trends, genetic variants and ligand target profiles. Diagrams illustrate receptor sequences (snake-plot and helix box diagrams) and relationships (phylogenetic trees).

Background and development

The GPCR database, GPCRdb was started in 1993 by Gert Vriend, Ad IJzerman, Bob Bywater and Friedrich Rippmann. Over two decades, GPCRdb evolved to be a comprehensive information system storing and analysing data. In 2013, the stewardship of GPCRdb was transferred to the David Gloriam group at the University of Copenhagen, backed up by an international team of contributors and developers from the EU COST Action ‘GLISTEN’. Today, GPCRdb offers reference data and easy-to-use web tools and diagrams for a multidisciplinary audience investigating GPCR function, drug design or evolution.

Content and features

A visual overview can be seen in the GPCRdb poster. The GPCRdb browsing system is structured on the following data content:

  • GPCRdb[2]
  • Receptors[3]
  • Signal Proteins[4]
  • Ligands[5]
  • Drugs[6]
  • Crystal Constructs
  • Tutorial

Each above menu item has subsections for data and tools.

Future directions

As part of two orphan GPCR projects funded by the European Research Commission and the Lundbeck Foundation, respectively, the GPCRdb will deposit data and develop computational tools for identification of endogenous and surrogate GPCR ligands. GPCRdb aims to grow from and enable new progress in GPCR structure, function and ligand design. It crosslinks to GuideToPharmacology database and has adopted the official NC-IUPHAR receptor naming nomenclature, has exchange with GPCR servers, and has also recently become part of the GPCR Consortium set out to generate an unprecedented number of crystal structures. Academic and industrial groups are welcome to contact us with suggestions of joint development or data deposition.

See also

References

  1. ↑ Isberg, Vignir; Vroling, Bas; Kant, Rob van der; Li, Kang; Vriend, Gert; Gloriam, David (2014-01-01). "GPCRDB: an information system for G protein-coupled receptors". Nucleic Acids Research. 42 (D1): D422–D425. doi:10.1093/nar/gkt1255. ISSN 0305-1048. PMC 3965068. PMID 24304901.
  2. ↑ Isberg, Vignir; Graaf, Chris de; Bortolato, Andrea; Cherezov, Vadim; Katritch, Vsevolod; Marshall, Fiona H.; Mordalski, Stefan; Pin, Jean-Philippe; Stevens, Raymond C. (2015-01-01). "Generic GPCR residue numbers – aligning topology maps while minding the gaps". Trends in Pharmacological Sciences. 36 (1). doi:10.1016/j.tips.2014.11.001. PMC 4408928. PMID 25541108.
  3. ↑ Hauser, Alexander S.; Chavali, Sreenivas; Masuho, Ikuo; Jahn, Leonie J.; Martemyanov, Kirill A.; Gloriam, David E.; Babu, M. Madan. "Pharmacogenomics of GPCR Drug Targets". Cell. doi:10.1016/j.cell.2017.11.033.
  4. ↑ Flock, Tilman; Hauser, Alexander S.; Lund, Nadia; Gloriam, David E.; Balaji, Santhanam; Babu, M. Madan (May 2017). "Selectivity determinants of GPCR–G-protein binding". Nature. 545 (7654): 317–322. doi:10.1038/nature22070. ISSN 1476-4687.
  5. ↑ Pándy-Szekeres, Gáspár; Munk, Christian; Tsonkov, Tsonko M.; Mordalski, Stefan; Harpsøe, Kasper; Hauser, Alexander S.; Bojarski, Andrzej J.; Gloriam, David E. "GPCRdb in 2018: adding GPCR structure models and ligands". Nucleic Acids Research. doi:10.1093/nar/gkx1109.
  6. ↑ Hauser, Alexander S.; Attwood, Misty M.; Rask-Andersen, Mathias; Schiöth, Helgi B.; Gloriam, David E. (December 2017). "Trends in GPCR drug discovery: new agents, targets and indications". Nature Reviews Drug Discovery. 16 (12): 829–842. doi:10.1038/nrd.2017.178. ISSN 1474-1784.
  • GPCRdb GPCR database
  • GLISTEN EU COST Action for GPCRs
  • GPCR-HGmod Predicted structure models of all GPCRs in human genome
  • GPCR-EXP Database for all experimentally solved GPCR structures
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