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Updated: Dec 7, 2025

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PROTAC-DB: an online database of PROTACs.

Gaoqi Weng1,2, Chao Shen1, Dongsheng Cao3

  • 1Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.

Nucleic Acids Research
|October 3, 2020
PubMed
Summary

PROTAC-DB is a new database for proteolysis-targeting chimeras (PROTACs), offering structural and experimental data to aid in rational PROTAC design. This resource supports the advancement of PROTAC technology for targeted protein degradation therapies.

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Area of Science:

  • Biochemistry
  • Medicinal Chemistry
  • Drug Discovery

Background:

  • Proteolysis-targeting chimeras (PROTACs) offer a novel therapeutic approach for targeted protein degradation.
  • Despite progress, PROTAC design remains challenging, hindering wider application.
  • Existing PROTACs have shown promise, with some entering clinical trials.

Purpose of the Study:

  • To establish PROTAC-DB, a comprehensive web-based database for PROTACs.
  • To integrate structural information and experimental data for rational PROTAC design.
  • To provide a freely accessible resource for researchers in the field.

Main Methods:

  • Development of a web-based database (PROTAC-DB).
  • Integration of chemical structures, biological activities, and physicochemical properties of PROTACs, warheads, E3 ligands, and linkers.
  • Implementation of text-based and structure-based search functionalities.
  • Inclusion of a filtering tool based on compound physicochemical properties.

Main Results:

  • PROTAC-DB currently contains 1662 PROTACs, 202 warheads, 65 E3 ligands, and 806 linkers.
  • The database includes data on chemical structures, biological activities, degradation capacities, binding affinities, and cellular activities.
  • Search functionalities include text-based (target, compound name/ID) and structure-based queries.
  • A filtering tool for physicochemical properties enhances result refinement.

Conclusions:

  • PROTAC-DB serves as a valuable, open-access resource for the PROTAC research community.
  • The database facilitates the rational design and development of novel PROTACs.
  • PROTAC-DB supports the advancement of targeted protein degradation as a therapeutic strategy.