pubchem-mcp-server

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Tools

Ten tools for querying PubChem's chemical information database:

Tool Name	Description
pubchem_search_compounds	Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.
pubchem_get_compound_details	Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.
pubchem_get_compound_image	Fetch a 2D structure diagram (PNG) for a compound by CID.
pubchem_get_compound_3d_structure	Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.
pubchem_get_compound_xrefs	Get external database cross-references (PubMed, patents, genes, proteins, etc.).
pubchem_get_compound_safety	Get GHS hazard classification and safety data for one or more compounds by CID (batch).
pubchem_get_bioactivity	Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.
pubchem_get_compound_interactions	Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.
pubchem_search_assays	Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).
pubchem_get_summary	Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

pubchem_search_compounds

Search PubChem for chemical compounds across five search modes.

• Identifier lookup — resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)
• Formula search — find compounds by molecular formula in Hill notation
• Substructure/superstructure — find compounds containing or contained within a query structure
• 2D similarity — find structurally similar compounds by Tanimoto similarity (configurable threshold)
• Optionally hydrate results with properties to avoid a follow-up details call

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pubchem_get_compound_details

Get detailed compound information by CID.

• Batches up to 100 CIDs in a single request
• 27 available properties: molecular weight, SMILES, InChIKey, XLogP, TPSA, complexity, stereo counts, and more
• Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View
• Optionally includes all known synonyms (trade names, systematic names, registry numbers)
• Optionally computes drug-likeness assessment (Lipinski Rule of Five + Veber rules) from fetched properties
• Optionally fetches pharmacological classification (FDA classes, mechanisms of action, MeSH classes, ATC codes)

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