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MCP live MCP 2026-07-28 http

pubchem-mcp-server

cyanheads/pubchem-mcp-server

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

Uptime
100.0%
1 direct probes · 30d
Response
805ms
last probe
Tools
10
callable
Resources
0
readable
Prompts
0
available
Primary URL
https://pubchem.caseyjhand.com/mcp

Tools · 10

pubchem_search_compounds

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 simila…

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, th…

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 SD…

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 wi…

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 …

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 (I…

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…

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 maxRes…

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.

How to use

Add to your Claude Desktop / Cursor / Cline MCP config:

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "url": "https://pubchem.caseyjhand.com/mcp",
      "transport": "http"
    }
  }
}