P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes

Yang Zhang; Xianrun Pan; Tianyu Shi; Zhifeng Gu; Zhaochang Yang; Minghao Liu; Yi Xu; Yu Yang; Liping Ren; Xiaoming Song; Hao Lin; Kejun Deng

doi:10.1016/j.jare.2023.10.012

P450Rdb: a manually curated database of reactions catalyzed by cytochrome P450 enzymes

J Adv Res. 2023 Oct 21:S2090-1232(23)00316-8. doi: 10.1016/j.jare.2023.10.012. Online ahead of print.

Authors

Yang Zhang¹, Xianrun Pan², Tianyu Shi³, Zhifeng Gu³, Zhaochang Yang³, Minghao Liu³, Yi Xu³, Yu Yang⁴, Liping Ren⁴, Xiaoming Song⁵, Hao Lin⁶, Kejun Deng⁷

Affiliations

¹ Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
² College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
³ School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
⁴ School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China.
⁵ School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China. Electronic address: songxm@ncst.edu.cn.
⁶ School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: hlin@uestc.edu.cn.
⁷ School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: dengkj@uestc.edu.cn.

PMID: 37871773
DOI: 10.1016/j.jare.2023.10.012

Abstract

Introduction: Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2%) have undergone functional characterization.

Objectives: To provide a convenient platform with abundant information on P450s and their corresponding reactions, we introduce the P450Rdb database, a manually curated resource compiles literature-supported reactions catalyzed by P450s.

Methods: All the P450s and Reactions were manually curated from the literature and known databases. Subsequently, the P450 reactions organized and categorized according to their chemical reaction type and site. The website was developed using HTML and PHP languages, with the MySQL server utilized for data storage.

Results: The current version of P450Rdb catalogs over 1,600 reactions, involving more than 590 P450s across a diverse range of over 200 species. Additionally, it offers a user-friendly interface with comprehensive information, enabling easy querying, browsing, and analysis of P450s and their corresponding reactions. P450Rdb is free available at http://www.cellknowledge.com.cn/p450rdb/.

Conclusions: We believe that this database will significantly promote structural and functional research on P450s, thereby fostering advancements in the fields of natural product synthesis, pharmaceutical engineering, biotechnological applications, agricultural and crop improvement, and the chemical industry.

Keywords: Cytochrome P450 enzymes; Reactions; database; products; substrates.