Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein–ligand interactions in PDB and PubChem

Abstract

Protein Data Bank Japan (https://pdbj.org/) is the Asian hub of three‐dimensional (3D) macromolecular structure data and a founding member of the global Protein Data Bank (PDB) network. Over two decades, we have curated and distributed experimentally determined structures, complementing international collaborations with Research Collaboratory for Structural Bioinformatics (RCSB) PDB, Biological Magnetic Resonance Data Bank, Protein Data Bank in Europe (PDBe), and Electron Microscopy Data Bank. In response to user demand for integrated structural and chemical data, we developed a new PubChem Portal that enables interactive exploration of compound‐protein interactions. Users can view ligand binding poses in 3D via our Web Graphics Library (WebGL)‐based Molmil viewer, with key interactions highlighted and key residues displayed in semi‐transparent stick models, enhanced through integration with secondary databases (e.g., Dynamics DB, eF‐site) for advanced insights into molecular dynamics and electrostatics. The system supports filtering by UniProt ID, Enzyme Commission (EC) number, Pfam ID, or PROSITE ID to identify structurally related compounds and visualizes protein–ligand interactions. A dynamic two‐dimensional (2D) Japan Agency for Medical Research and Development representation enables real‐time atom‐level navigation, with clickable atoms linking to 3D structures. This tool allows users to explore compound‐protein interaction landscapes, identify potential binding modes, and guide experimental design, such as mutagenesis or crystallization. The portal offers a comprehensive, user‐centered ecosystem that bridges chemical and structural data, enhancing access to biological insights through integrated visualization and analysis.