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  What is CovalentInDB


CovalentInDB (Covalent Inhibitor Database) is the largest web-accessible resource for covalent inhibitors and related targets. The latest version provides the information for 8544 covalent inhibitors and 343 related protein targets collected by comprehensive literature searching.

CovalentInDB provides not only the basic information of covalent inhibitors, targets, and bioactivity, but also the reactive warheads of inhibitors, covalent reaction mechanism, attacked nucleophilic residues and covalent-mechanism experimental verification methods. A molecular visualization function is also embedded to display protein-ligand interaction.



2023/12/27: We've enhanced the accessibility of the data by restructuring the downloadable files. Now, the entire database is available for download with a single click.

  Feature 1: Covalent-binding Complexes


A new form of data, the cocrystal structures of covalent ligand-protein complexes (2620), was added to our database. We made a systematic analysis of protein-ligand binding mode for each complex and a pharmacophore model was also proposed based on the protein-ligand interactions, which was dedicated to provide useful information for the structure-based rational design of targeted covalent inhibitors.

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  Feature 2: Proteome-wide Profiled Covalent Binding Sites


A lack of the knowledge of covalent binding sites has limited the development of covalent ligands. In order to expand the research of covalent ligands to the proteome-level, we profiled the entire structures in RCSB Protein Data Bank (PDB) with an well-validated AI model (DeepCoSI) to evaluate the ligandability of each cysteine for covalent ligand design.
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Cite CovalentInDB: Du, H., Gao, J., Weng, G., Ding, J., Chai, X., Pang, J., Kang, Y., Li, D., Cao, D., & Hou, T. (2021). CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic acids research, 49(D1), D1122–D1129. https://doi.org/10.1093/nar/gkaa876