Connect Pubchem and your agent gets 10 tools, among them pubchem_get_bioactivity, pubchem_get_compound_3d_structure, pubchem_get_compound_details. It answers at https://pubchem.caseyjhand.com/mcp over streamable HTTP, and it listed its tools to an anonymous client, so no sign-in was needed for that. Our probes reached it 6 of 6 times since 11 September 2026; the last check, on 21 October 2026, succeeded.
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Description as the publisher wrote it.
| Tool | What it does |
|---|---|
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 Inputs: cid, outcomeFilter, targetGeneId, targetAccession, offset, maxResults |
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, rende Inputs: cid, format, includeAlternateConformerIds, maxAtoms, maxBonds, includeRawSdf |
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-lik Inputs: cids, properties, includeDescription, descriptionOffset, maxDescriptions, includeSynonyms |
pubchem_get_compound_image | Fetch a 2D structure diagram (PNG image) for a compound by CID. Inputs: cid, size |
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 pag Inputs: cid, kinds, offset, maxEntries |
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. Data sourced fro Inputs: cids |
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 I Inputs: cid, xrefTypes, offset, maxPerType |
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. Inputs: entityType, identifiers |
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 Inputs: targetType, targetQuery, offset, maxResults |
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 similarity. Returns a page of CIDs — reach mat Inputs: searchType, identifierType, identifiers, formula, allowOtherElements, query |
Every block below points at https://pubchem.caseyjhand.com/mcp. Pick your client and copy.
claude mcp add --transport http pubchem https://pubchem.caseyjhand.com/mcp
{
"mcpServers": {
"pubchem": {
"command": "npx",
"args": ["-y", "mcp-remote", "https://pubchem.caseyjhand.com/mcp"]
}
}
}{
"mcpServers": {
"pubchem": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"servers": {
"pubchem": {
"type": "http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"context_servers": {
"pubchem": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"mcpServers": {
"pubchem": {
"serverUrl": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"mcpServers": {
"pubchem": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}name: Pubchem
version: 0.0.1
schema: v1
mcpServers:
- name: Pubchem
type: streamable-http
url: https://pubchem.caseyjhand.com/mcp{
"mcpServers": {
"pubchem": {
"httpUrl": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"mcpServers": {
"pubchem": {
"type": "http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}{
"mcpServers": {
"pubchem": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}goose://extension?url=https%3A%2F%2Fpubchem.caseyjhand.com%2Fmcp&type=streamable_http&id=pubchem&name=Pubchem
It answered our last check on 21 October 2026 in 604 ms. Over 6 checks since 11 September 2026 it answered 6. Status here comes from Neuronto's own probes, not from the publisher.
10, as returned by the server's own tools/list on 13 September 2026: pubchem_get_bioactivity, pubchem_get_compound_3d_structure, pubchem_get_compound_details, pubchem_get_compound_image, pubchem_get_compound_interactions, pubchem_get_compound_safety, pubchem_get_compound_xrefs, pubchem_get_summary, and 2 more.
It answered our last check on 21 October 2026 in 604 ms. Over 6 checks since 11 September 2026 it answered 6.
Put the server under mcpServers in ~/.cursor/mcp.json with the URL https://pubchem.caseyjhand.com/mcp. The exact JSON is above, with the same setup for Claude Code, Claude Desktop, VS Code, Windsurf, Zed, Gemini CLI and the rest.
It listed its tools to an anonymous client, so reading the tool list needs no key. Individual tools can still ask for credentials in their own inputs.
Publisher: io.github.cyanheads. Endpoint host: pubchem.caseyjhand.com. ARD identifier: urn:air:io.github.cyanheads:mcp:pubchem-mcp-server.
First indexed 10 September 2026. The tools are exactly what the server returned; nothing on this page
is inferred from its name. Ranking in Neuronto search is never for sale.