BindingDB database of measured binding affinities

BindingDB database of measured binding affinities provides experimentally measured binding affinities linking protein targets (including isoforms and mutational variants) and small-molecule ligands to support drug discovery and mechanistic studies.

Key Features:

• Data content: Approximately 20,000 experimentally determined binding affinities for around 110 distinct protein targets, including isoforms and mutational variants.
• Ligand set: Information on roughly 11,000 small-molecule ligands curated from the scientific literature.
• Target focus: Proteins are primarily drug-targets or candidate drug-targets with associated structural data in the Protein Data Bank (PDB).
• Search capabilities: Queries supported by chemical structure, substructure, similarity, protein sequence, ligand and protein names, affinity ranges, and molecular weight.
• Cross-references: Data linked to structural records via Protein Data Bank IDs (PDB IDs) and to bibliographic records via PubMed IDs.
• Data export: Query results downloadable as annotated SDfiles suitable for downstream analysis and for use in virtual screening of uploaded compound databases.

Scientific Applications:

• Drug discovery: Inform lead identification and optimization by providing quantitative protein–ligand affinity data.
• Computational modeling: Provide training and validation data for QSAR, docking, and machine-learning models of binding affinity.
• Structure–function analysis: Enable correlation of binding affinities with available PDB structural data for mechanistic studies.
• High-throughput screening support: Supply curated ligand sets and affinity ranges for virtual screening and prioritization workflows.
• Pharmacology and medicinal chemistry: Support SAR analysis and target characterization with experimentally measured affinities.

Methodology:

Searchable database queries by chemical structure/substructure/similarity, protein sequence, ligand and protein names, affinity ranges, and molecular weight; data linked via PDB IDs and PubMed IDs; query results exportable as annotated SDfiles for downstream analyses or virtual screening.