Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.
claude mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcpcodex mcp add pubchem-mcp-server --url https://pubchem.caseyjhand.com/mcp{
"mcpServers": {
"pubchem-mcp-server": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}gemini mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcp{
"mcpServers": {
"pubchem-mcp-server": {
"command": "bunx",
"args": [
"mcp-remote",
"https://pubchem.caseyjhand.com/mcp"
]
}
}
}{
"mcpServers": {
"pubchem-mcp-server": {
"type": "http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}curl -X POST https://pubchem.caseyjhand.com/mcp \
-H "Content-Type: application/json" \
-H "MCP-Protocol-Version: 2026-07-28" \
-d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2026-07-28","capabilities":{},"clientInfo":{"name":"curl","version":"1.0.0"}}}'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.
Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.
Fetch a 2D structure diagram (PNG image) for a compound by CID.
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).
Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.
Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.
Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".
Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.
Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.
No tools match the current filter.
Core physicochemical properties for a PubChem compound by CID. Use pubchem_get_compound_details to select properties or add descriptions, synonyms, drug-likeness, and classification.
GHS hazard classification for a PubChem compound by CID — signal word, pictograms, hazard (H) and precautionary (P) statements. Not every compound carries a deposited classification.
A 2D structure diagram (PNG, 300x300) for a PubChem compound by CID. Use pubchem_get_compound_image to choose the image size.
External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and to page through the rest with offset.
Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target, raise the cap, and page through the rest with offset.
Summary for a PubChem BioAssay by AID — name, description, source, protocol, and substance counts.