{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T22:29:59Z","timestamp":1786228199939,"version":"3.56.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,9,28]],"date-time":"2021-09-28T00:00:00Z","timestamp":1632787200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["201908080143"],"award-info":[{"award-number":["201908080143"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001655","name":"German Academic Exchange Service","doi-asserted-by":"publisher","award":["91653768"],"award-info":[{"award-number":["91653768"]}],"id":[{"id":"10.13039\/501100001655","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["RTG 2202"],"award-info":[{"award-number":["RTG 2202"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Baden-W\u00fcrttemberg Ministry of Science, Research and Art"},{"DOI":"10.13039\/501100002714","name":"University of Freiburg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002714","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In recent years, the drug discovery paradigm has shifted toward compounds that covalently modify disease-associated target proteins, because they tend to possess high potency, selectivity, and duration of action. The rational design of novel targeted covalent inhibitors (TCIs) typically starts from resolved macromolecular structures of target proteins in their apo or holo forms. However, the existing TCI databases contain only a paucity of covalent protein\u2013ligand (cP\u2013L) complexes. Herein, we report CovPDB, the first database solely dedicated to high-resolution cocrystal structures of biologically relevant cP\u2013L complexes, curated from the Protein Data Bank. For these curated complexes, the chemical structures and warheads of pre-reactive electrophilic ligands as well as the covalent bonding mechanisms to their target proteins were expertly manually annotated. Totally, CovPDB contains 733 proteins and 1,501 ligands, relating to 2,294 cP\u2013L complexes, 93 reactive warheads, 14 targetable residues, and 21 covalent mechanisms. Users are provided with an intuitive and interactive web interface that allows multiple search and browsing options to explore the covalent interactome at a molecular level in order to develop novel TCIs. CovPDB is freely accessible at http:\/\/www.pharmbioinf.uni-freiburg.de\/covpdb\/ and its contents are available for download as flat files of various formats.<\/jats:p>","DOI":"10.1093\/nar\/gkab868","type":"journal-article","created":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T19:23:18Z","timestamp":1631733798000},"page":"D445-D450","source":"Crossref","is-referenced-by-count":51,"title":["CovPDB: a high-resolution coverage of the covalent protein\u2013ligand interactome"],"prefix":"10.1093","volume":"50","author":[{"given":"Mingjie","family":"Gao","sequence":"first","affiliation":[{"name":"Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universit\u00e4t Freiburg, Hermann-Herder-Stra\u00dfe 9, D-79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6034-2016","authenticated-orcid":false,"given":"Aur\u00e9lien\u00a0F\u00a0A","family":"Moumbock","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universit\u00e4t Freiburg, Hermann-Herder-Stra\u00dfe 9, D-79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ammar","family":"Qaseem","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universit\u00e4t Freiburg, Hermann-Herder-Stra\u00dfe 9, D-79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianqing","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universit\u00e4t Freiburg, Hermann-Herder-Stra\u00dfe 9, D-79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3744-189X","authenticated-orcid":false,"given":"Stefan","family":"G\u00fcnther","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universit\u00e4t Freiburg, Hermann-Herder-Stra\u00dfe 9, D-79104 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,28]]},"reference":[{"key":"2022010507311776700_B1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1016\/j.drudis.2015.05.005","article-title":"Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies","volume":"20","author":"Bauer","year":"2015","journal-title":"Drug Discov. 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