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. 2025 Jan 6;53(D1):D1510-D1515.
doi: 10.1093/nar/gkae768.

PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters

Jingxuan Ge  1   2 , Shimeng Li  1 , Gaoqi Weng  1 , Huating Wang  1 , Meijing Fang  3 , Huiyong Sun  4 , Yafeng Deng  2 , Chang-Yu Hsieh  1 , Dan Li  1 , Tingjun Hou  1   3
Affiliations

PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters

Jingxuan Ge et al. Nucleic Acids Res. .

Abstract

Proteolysis-targeting chimera (PROTAC) is an emerging therapeutic technology that leverages the ubiquitin-proteasome system to target protein degradation. Due to its event-driven mechanistic characteristics, PROTAC has the potential to regulate traditionally non-druggable targets. Recently, AI-aided drug design has accelerated the development of PROTAC drugs. However, the rational design of PROTACs remains a considerable challenge. Here, we present an updated online database, PROTAC-DB 3.0. In this third version, we have expanded the database to include 6111 PROTACs (87% increase compared to the 2.0 version). Additionally, the database now contains 569 warheads (small molecules targeting the protein), 2753 linkers, and 107 E3 ligands (small molecules recruiting E3 ligases). The number of target-PROTAC-E3 ternary complex structures has also increased to 959. Recognizing the importance of druggability in PROTAC design, we have incorporated pharmacokinetic data to PROTAC-DB 3.0. To enhance user experience, we have added features for sorting based on molecular similarity and literature publication date. PROTAC-DB 3.0 is accessible at http://cadd.zju.edu.cn/protacdb/.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Pharmacokinetic parameter tabs in the detailed information pages of PROTACs.
Figures 2.
Figures 2.
(A) and (B) demonstrate the use of the search bar on both the main page and the browse page. (C) shows the results of the search sorted by molecular similarity.
Figures 3.
Figures 3.
Search page results are sorted on literature publication date.
See this image and copyright information in PMC

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