TPDdb: the comprehensive database of targeted protein degrader

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-10-15 DOI:10.1093/nar/gkaf996

Xinran Qin, Yinpeng Zhang, Yajunzi Wang, Yintao Zhang, Jiachen Jing, Yuyuan Zhang, Gaoxiang Xu, Haoping Teng, Tianjun Wang, Lei Fu, Ying Zhou, Xin Liu, Feng Zhu

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引用次数: 0

Abstract

Targeted protein degraders (TPDs) have emerged in the past decade as a new drug modality of transformative paradigm, offering a powerful strategy to catalytically remove disease-relevant proteins, especially those long considered as “undruggable.” With the rapid advancement in this direction, there is increasing demand for a database describing TPDs. Herein, a comprehensive database of TPDs, titled TPDdb, was therefore developed. TPDdb is unique in (i) covering the largest amount of TPDs among existing databases (6002 Molecular Glues, 22 183 PROTACs, 249 LYTACs, 169 ATTECs, 29 AUTOTACs, and 23 AUTACs targeting 580 proteins of interest and associated with 274 diseases) with their structural and physicochemical properties offered; (ii) describing 27 796 activities (IC50, DC50, Dmax, etc.) for all collected TPDs related to 201 cell lines; and (iii) providing the structures of TPDs, proteins of interest, ligase, and experimentally determined ternary complexes. TPDdb is now accessible at https://idrblab.org/TPDdb/

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TPDdb：靶向蛋白降解物综合数据库

靶向蛋白降解物（Targeted protein degradation, TPDs）在过去十年中作为一种新的药物模式出现，提供了一种强大的策略来催化去除疾病相关蛋白，特别是那些长期以来被认为是“不可药物”的蛋白。随着这一方向的快速发展，对描述tpd的数据库的需求越来越大。因此，开发了一个名为TPDdb的综合tppd数据库。TPDdb的独特之处在于(i)在现有数据库中覆盖了最多的TPDs （6002 Molecular glue, 22 183 PROTACs, 249 lytac, 169 attec， 29 autotac和23 AUTACs，针对580种感兴趣的蛋白质，与274种疾病相关），并提供了它们的结构和物理化学性质；（ii）描述所有收集到的与201个细胞系相关的TPDs的27796个活性（IC50、DC50、Dmax等）；（iii）提供tpd、感兴趣的蛋白质、连接酶和实验确定的三元配合物的结构。tpdb现在可以在https://idrblab.org/TPDdb/上访问

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.