Compounds
Chemical structures, molecular identifiers, physicochemical properties, and associated protein targets.
NPIMDB (Nucleic acid–Protein Interaction Modulators Database) is a curated, structure-based database of small molecules associated with nucleic acid–protein interaction (NPI) sites. It integrates molecular, protein, and binding-pocket information to support computational and experimental drug discovery.
NPIMDB organizes curated data into interconnected compound, protein, and binding-pocket records, providing access to chemical and structural information through an interactive web interface.
Chemical structures, molecular identifiers, physicochemical properties, and associated protein targets.
UniProt identifiers, functional annotations, associated compounds, and nucleic acid–binding information.
PDB structures, ligand-contacting residues, nucleic acid–binding sites, and interactive 3D structural visualization.
NPIMDB was constructed through systematic analysis of experimentally determined structures from the Protein Data Bank (PDB), supported by UniProt annotations and SIFTS residue mappings.
Retrieve protein–nucleic acid and protein–small molecule complexes from the PDB.
Identify nucleic acid–contacting residues and map them to UniProt protein sequences.
Define ligand-binding residues within 4 Å and evaluate overlap with nucleic acid–binding sites.
Filter non-relevant ligands, classify compounds, and link curated pockets to proteins.
NPIMDB supports the exploration of small molecules targeting nucleic acid–protein interfaces, structural characterization of binding pockets, and the development and benchmarking of molecular docking, virtual screening, and AI-driven drug discovery methods.
Broad functional classification of 77 NPI-associated proteins based on InterPro family/domain annotations and manual curation.
| Broad protein class | Count | Percentage |
|---|---|---|
| RNA-binding / RNA metabolism protein | 17 | 22.1% |
| Nuclease / DNA-RNA repair enzyme | 13 | 16.9% |
| DNA/RNA polymerase and replication protein | 11 | 14.3% |
| Viral replication / viral nucleic-acid-related protein | 7 | 9.1% |
| tRNA-related enzyme | 6 | 7.8% |
| Other enzyme / miscellaneous | 6 | 7.8% |
| Transcription factor / transcription regulator | 5 | 6.5% |
| Translation / ribosomal protein | 5 | 6.5% |
| DNA/RNA modification or nucleotide metabolism enzyme | 4 | 5.2% |
| CRISPR-Cas / prokaryotic antiviral defense protein | 2 | 2.6% |
| Argonaute / RNAi-related protein | 1 | 1.3% |
| Total | 77 | 100% |