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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 8561 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.
2022/06/27: Check new features in the latest version of our database.
Feature 1: Covalent-binding Complexes
A new form of data, the cocrystal structures of covalent ligand-protein complexes (2834), 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.
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.
