Amide scaffolds identified in ChEMBL database

This dataset provides a comprehensive and curated knowledgebase of amide moieties systematically extracted from the ChEMBL database (version 36). Amide functional groups are ubiquitous in medicinal chemistry, and this resource is designed to support rational drug design through scaffold hopping and multi-objective optimization.

Data Content and Organization

The repository includes several key components:

• The Global Amide Scaffold Library: A curated set of 17,769 unique C(=O)N scaffolds, each annotated with precisely defined substitution sites (growth vectors). To ensure full traceability, every scaffold is explicitly linked to its parent compounds and their corresponding ChEMBL identifiers.
• High-Confidence Research Subset: A refined collection of scaffolds derived from high-confidence bioactivity data. This subset includes granular annotations such as Target IDs, associated Compound IDs, and SMILES strings, specifically structured to facilitate alternative scaffold hopping and complex multi-target compound design.
• Practical Implementation Tools: To bridge the gap between data and application, an exemplary KNIME workflow is provided. This workflow demonstrates a standardized protocol for designing analogs using diverse C(=O)N scaffolds, using BTK (Bruton’s tyrosine kinase) inhibitors as a representative case study for non-covalent ligand optimization.