TPDdb: the comprehensive database of targeted protein degrader

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

doi:10.1093/nar/gkaf996

TPDdb: the comprehensive database of targeted protein degrader

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^*

^*Corresponding author for this work

AoPHA Faculty

Research output: Contribution to journal › Article › peer-review

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/

Original language	English
Pages (from-to)	gkaf996
Journal	Nucleic Acids Research
DOIs	https://doi.org/10.1093/nar/gkaf996
Publication status	Published - 2025

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10.1093/nar/gkaf996

Cite this

@article{94cdde7c1c4c4c27aa51af616a409277,

title = "TPDdb: the comprehensive database of targeted protein degrader",

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/",

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

year = "2025",

doi = "10.1093/nar/gkaf996",

language = "English",

pages = "gkaf996",

journal = "Nucleic Acids Research",

issn = "1362-4962",

}

TY - JOUR

T1 - TPDdb: the comprehensive database of targeted protein degrader

AU - Qin, Xinran

AU - Zhang, Yinpeng

AU - Wang, Yajunzi

AU - Zhang, Yintao

AU - Jing, Jiachen

AU - Zhang, Yuyuan

AU - Xu, Gaoxiang

AU - Teng, Haoping

AU - Wang, Tianjun

AU - Fu, Lei

AU - Zhou, Ying

AU - Liu, Xin

AU - Zhu, Feng

PY - 2025

Y1 - 2025

N2 - 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/

AB - 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/

U2 - 10.1093/nar/gkaf996

DO - 10.1093/nar/gkaf996

M3 - Article

SN - 1362-4962

SP - gkaf996

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -