UbiHub: a data hub for the explorers of ubiquitination pathways
Open accessAbstract
Motivation: Protein ubiquitination plays a central role in important cellular machineries such as protein degradation or chromatin-mediated signaling. With the recent discovery of the first potent ubiquitin-specific protease inhibitors, and the maturation of proteolysis targeting chimeras as promising chemical tools to exploit the ubiquitin-proteasome system, protein target classes associated with ubiquitination pathways are becoming the focus of intense drug-discovery efforts. Results: We have developed UbiHub, an online resource that can be used to visualize a diverse array of biological, structural and chemical data on phylogenetic trees of human protein families involved in ubiquitination signaling, including E3 ligases and deubiquitinases. This interface can inform target prioritization and drug design, and serves as a navigation tool for medicinal chemists, structural and cell biologists exploring ubiquitination pathways. Availability and implementation: https://ubihub.thesgc.org.
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Fewer than 10 of the more than 600 human E3 ubiquitin ligases have so far been exploited for targeted protein degradation by small molecules.
“Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity.”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [55]
About 270 of the 632 or more human E3 ligases are currently believed to be involved in the ubiquitin-proteasome system, based on annotations from UniProt and the Reactome Pathway database.
“Based on the annotations of E3 ligases and their binding partners available from UniProt and the Reactome Pathway database, about 270 of the 632 or more human E3 ligases are currently believed to be involved in the UPS 55 .”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [55]
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- Authors
- Liu, L., Damerell, D. R., Koukouflis, L., Tong, Y., Marsden, B. D., & Schapira, M.
- Affiliations
- University of Toronto (CA)
- University of Oxford (GB)
- Corresponding author
- Schapira, Matthieu
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-01-02
- Volume
- 35
- Issue
- 16
- Pages
- 2882-2884
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6691330
- OpenAlex
- W2907957654
- Cited by
- 76
- References
- 30
- Citations by year
- 2026: 15 · 2025: 14 · 2024: 12 · 2023: 11 · 2022: 11 · 2021: 6 · 2020: 6 · 2019: 1
- FWCI
- 1.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Structural Genomics Consortium
- SGC
- AbbVie
- Bayer Pharma AG
- Boehringer Ingelheim
- Canada Foundation for Innovation
- Eshelman Institute for Innovation
- Ontario Genomics Institute (OGI-055)
- Innovative Medicines Initiative
- EU/EFPIA
- ULTRA-DD (115766)
- Janssen
- Merck KGaA
- Novartis Pharma AG
- Ontario Ministry of Research, Innovation and Science
- Pfizer
- São Paulo Research Foundation-FAPESP
- Takeda
- The Wellcome (106169/ZZ14/Z)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- ubiquitination, ubiquitin-proteasome system, E3 ubiquitin ligase, deubiquitinase, phylogenetic tree, protein families, PROTACs, drug target prioritization, drug design
- MeSH terms
- Humans, Phylogeny, Ubiquitin-Protein Ligases, Ubiquitination, Proteolysis
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