io.github.cyanheads/pubchem-mcp-server · v0.7.0 · health-and-science
io.github.cyanheads/pubchem-mcp-server is healthy: it completed an MCP handshake in 2416 ms and exposes 10 tools.
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Endpoint: https://pubchem.caseyjhand.com/mcp (streamable-http)
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| Users (last 30 days) | 0 |
| Handshake | Healthy |
| Auth needed | None |
| Tool count | 10 |
| Latency | 2416 ms |
| Last checked (UTC) | 2026-10-15T03:25:46.756Z |
| Checked (UTC) | Status | Latency | Error |
|---|---|---|---|
| 2026-10-15T03:25:46.756Z | Healthy | 2416 |
pubchem_search_compounds | Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach matches |
pubchem_get_compound_details | 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 pharmacologi |
pubchem_get_compound_image | Fetch a 2D structure diagram (PNG image) for a compound by CID. |
pubchem_get_compound_3d_structure | 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 conform |
pubchem_get_compound_xrefs | 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. PubMed IDs come highest (most re |
pubchem_get_compound_safety | 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, merged across sources, plus each source's own classification — its signal wo |
pubchem_get_bioactivity | 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 |
pubchem_get_compound_interactions | 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 offse |
pubchem_search_assays | 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. |
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; identifiers past that are returned in unprocessed for a follow-up call. |