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. 2021 Jan 8;49(D1):D1381-D1387.
doi: 10.1093/nar/gkaa807.

PROTAC-DB: an online database of PROTACs

Gaoqi Weng  1   2 , Chao Shen  1 , Dongsheng Cao  3 , Junbo Gao  1 , Xiaowu Dong  1 , Qiaojun He  1 , Bo Yang  1 , Dan Li  1 , Jian Wu  4 , Tingjun Hou  1   2
Affiliations

PROTAC-DB: an online database of PROTACs

Gaoqi Weng et al. Nucleic Acids Res. .

Abstract

Proteolysis-targeting chimeras (PROTACs), which selectively degrade targeted proteins by the ubiquitin-proteasome system, have emerged as a novel therapeutic technology with potential advantages over traditional inhibition strategies. In the past few years, this technology has achieved substantial progress and two PROTACs have been advanced into phase I clinical trials. However, this technology is still maturing and the design of PROTACs remains a great challenge. In order to promote the rational design of PROTACs, we present PROTAC-DB, a web-based open-access database that integrates structural information and experimental data of PROTACs. Currently, PROTAC-DB consists of 1662 PROTACs, 202 warheads (small molecules that target the proteins of interest), 65 E3 ligands (small molecules capable of recruiting E3 ligases) and 806 linkers, as well as their chemical structures, biological activities, and physicochemical properties. Except the biological activities of warheads and E3 ligands, PROTAC-DB also provides the degradation capacities, binding affinities and cellular activities for PROTACs. PROTAC-DB can be queried with two general searching approaches: text-based (target name, compound name or ID) and structure-based. In addition, for the convenience of users, a filtering tool for the searching results based on the physicochemical properties of compounds is also offered. PROTAC-DB is freely accessible at http://cadd.zju.edu.cn/protacdb/.

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Figures

Graphical Abstract
Graphical Abstract
The three basic steps to construct PROTAC-DB: (I) literature searching, (II) data collection, and (III) data processing by separating PROTACs into warheads, E3 ligands and linkers.
Figure 1.
Figure 1.
The basic data collection and processing stages of PROTAC-DB: (I) the literature searching stage, (II) the data collection stage and (III) the data processing stage by separating PROTACs into warheads, E3 ligands and linkers.
Figure 2.
Figure 2.
The query or browsing results and the filtering tool for the PROTAC dataset.
Figure 3.
Figure 3.
(A) Summary and (B) activity data tabs in the detailed information pages of PROTACs.
Figure 4.
Figure 4.
(A) Summary and (B) PROTAC tabs in the detailed information pages of warheads.
See this image and copyright information in PMC

References

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