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What is CovalentInDB
CovalentInDB (Covalent Inhibitor Database) is the largest web-accessible
resource for covalent inhibitors
and related targets.
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.
2024/06/20: We are excited to introduce CovalentInDB 2.0 with its enhanced features. Please
explore the new capabilities. We are continually reviewing and updating the database, so the
data will be periodically updated in the near future.
Feature 1: Covalent-binding Complexes
A new form of data, the cocrystal structures of 3445 covalent ligand-protein complexes,
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.
Feature 3: Natural Compounds with Covalent Binding Potential
Natural compounds have long been recognized for their therapeutic potential and are a
cornerstone in the search for new drugs. By analyzing the covalent binding capabilities of these
compounds, we aim to uncover new opportunities for drug discovery and development. Our rigorous
analysis identifies 105,901 natural compounds with promising covalent binding warheads,
adding a
valuable layer of information for researchers and developers.
Explore
the data! to leverage the power of natural compounds in your research and drug discovery
efforts.
Feature 4: Covalent Virtual Screening Library
We are the first to analyze commercially-available compounds, identifying 2,030,192
in-stock compounds with covalent binding warheads. For each compound, we predicted ADMET
(Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties using ADMETLab 2.0.
This curated Covalent Virtual Screening Library is a significant tool for the covalent drug
discovery community, providing detailed data to support the development of novel therapeutics.
Explore
the library! to leverage extensive data for innovative covalent inhibitor research.
Feature 5: Data Upload Feature
To leverage the collective expertise of the scientific community and facilitate timely updates
to the database, we have implemented a user data upload feature. All user-submitted
data undergo
a thorough manual review to ensure accuracy and quality before being incorporated into the
database.
Cite CovalentInDB:
Du, H., Zhang, X., Wu, Z., Zhang, O., Gu, S., Wang, M., Zhu, F., Li, D., Hou, T., & Pan, P. (2024). CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening. Nucleic acids research, gkae946. Advance online publication. https://doi.org/10.1093/nar/gkae946