CovBinderInPDB

CovBinderInPDB provides a curated database of covalent residue–binder adducts extracted from RCSB Protein Data Bank (PDB) mmCIF files to support structure-based design and benchmarking of target-specific covalent modulators.

Key Features:

• Data Source and Extraction: Extracts records from RCSB Protein Data Bank (PDB) mmCIF files and identifies covalent bonds indicating side chain modifications of amino acid residues by covalent binders.
• Data Cleaning and Recovery: Recovers residue–binder adducts using the PDB Chemical Component Dictionary to represent chemical interactions between targeted residues and covalent binders.
• Curated Database Content: Contains 7,375 covalent modifications involving 2,189 unique covalent binders targeting nine residue types (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, Tyr) derived from 3,555 complex structures of 1,170 unique protein chains.
• Pre-reaction Form Curation: Uses multiple curation strategies to recover and represent pre-reaction forms of covalent binders from adducts.

Scientific Applications:

• Computational method development: Enables development and benchmarking of computational strategies for designing covalent modulators using experimentally observed covalent interactions.
• Structure-based design: Supports structure-based rational design of target-specific covalent modulators by providing residue-level covalent modification data.
• Disciplinary research support: Provides a dataset for computational chemistry, structural biology, and pharmacology studies of covalent inhibitor interactions.

Methodology:

Data were extracted from RCSB PDB mmCIF files by identifying covalent-bond records indicating side-chain modifications; residue–binder adducts were recovered using the PDB Chemical Component Dictionary; pre-reaction forms of covalent binders were curated from the adducts.