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Updated: Aug 19, 2025

Covalent Fragment Screening Using the Quantitative Irreversible Tethering Assay

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Published on: February 28, 2025

CovBinderInPDB: A Structure-Based Covalent Binder Database.

Xiao-Kang Guo¹, Yingkai Zhang^1,2,3

¹Department of Chemistry, New York University, New York, New York 10003, United States.

Journal of Chemical Information and Modeling

|December 1, 2022

Summary

This summary is machine-generated.

Researchers developed a computational method to identify specific covalent binders for drug discovery. This curated database aids in designing targeted covalent modulators for improved drug specificity and efficacy.

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Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Covalent inhibition is a powerful drug discovery strategy.
Achieving target specificity with covalent modulators remains a significant challenge.
Structure-based rational design is crucial for developing specific covalent drugs.

Purpose of the Study:

To develop an integrated computational protocol for curating covalent binders from the Protein Data Bank (PDB).
To create a comprehensive database of covalent modifications for structure-based drug design.
To facilitate the development and benchmarking of computational strategies for covalent modulator design.

Main Methods:

Collected and cleaned covalent bond records from PDB macromolecular crystallographic information files (mmCIF).
Recovered residue-binder adducts using the PDB Chemical Component Dictionary.
Employed strategies to curate pre-reaction forms of covalent binders from adducts.

Main Results:

Developed the CovBinderInPDB database containing 7375 covalent modifications.
Identified 2189 unique covalent binders targeting nine amino acid residue types.
Data sourced from 3555 complex structures involving 1170 unique protein chains.

Conclusions:

The CovBinderInPDB database provides a foundation for covalent modulator design.
Enables the development and benchmarking of computational approaches for target-specific covalent drugs.
The database is freely accessible for research purposes.