MCP SERVERFind a compound in PubChem by name, SMILES, InChIKey, formula, substructure or similarity, then pull its properties, 3D conformer, GHS hazards, bioactivity and interactions.
LABSCO SUMMARY
Every list-returning tool reports the total beside the page it gave you and takes an offset to reach the rest, so an agent can tell a short answer from a complete one — cross-references and interactions even page per type, each with its own total. Search can hydrate results with properties in the same call, which removes the usual second trip through the detail tool. The gaps that remain belong to the data, not the server: not every compound has computed 3D coordinates, and interaction coverage is richest for approved drugs.
A read-only client for PubChem's compound, assay and safety data — ten tools covering search, structure retrieval and every record that hangs off a CID. The same records are also exposed as URI-templated resources such as pubchem://compound/{cid}/safety.
No account and no key — PubChem's API is open. Run it locally over stdio with bunx @cyanheads/pubchem-mcp-server@latest, which needs Bun v1.3.0 or higher (or Node.js v24+); the same package serves Streamable HTTP on port 3010 at /mcp when you want it over the network. A public hosted instance at https://pubchem.caseyjhand.com/mcp takes a Streamable HTTP client with nothing installed. The detail tools work from CIDs, so a search comes first unless you already hold one.
One command — npx -y @cyanheads/pubchem-mcp-server
USE CASES
Resolve up to 25 names, SMILES or InChIKeys to CIDs in one call, then pull properties for the batch.
Get the Lipinski and Veber assessment alongside the properties it was computed from, then look at what assays already tested it.
Pull GHS signal word, pictograms and H- and P-codes for several compounds at once, with the depositor named for each.
Run a Tanimoto similarity or substructure search, then compare the hits on the properties that matter.
Fetch the default 3D conformer as raw SDF and pass it straight through, or as parsed atoms and bonds to reason over first.
Search assays by gene symbol or UniProt accession, then read the summary of the ones worth opening.
Counted once with only startup setup. Other versions, modes or optional credentials may expose a different list.
pubchem_get_bioactivityGet 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?".
pubchem_get_compound_3d_structureGet 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).
pubchem_get_compound_detailsGet 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.
pubchem_get_compound_imageFetch a 2D structure diagram (PNG image) for a compound by CID.
pubchem_get_compound_interactionsGet 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.
pubchem_get_compound_safetyGet 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.
pubchem_get_compound_xrefsGet 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.
pubchem_get_summaryGet 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.
pubchem_search_assaysFind 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.
pubchem_search_compoundsSearch 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.
BEFORE YOU INSTALL
10 tools when we connected. All ten tools are read-only and idempotent.
npx on PATH
The documented client connects to a hosted endpoint.
CONTEXT COST
Rated by the size of the 10 tool definitions that ride along on every turn, not by how many there are
INSTALLATION
npx -y @cyanheads/pubchem-mcp-serverhttps://pubchem.caseyjhand.com/mcpAdd this hosted endpoint to your MCP client.
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "streamable-http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}Clients spell the "type" value differently: Claude Code and VS Code use "http", Cline uses "streamableHttp", and Roo Code uses "streamable-http". Claude Desktop does not accept a URL entry in its config file; remote servers go under Settings → Connectors.
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