How to connect
Same URL, five paste targets. Ready surface · Auth required. Not a safe-to-install badge. Handshake this URL
Paste into Settings → MCP or .cursor/mcp.json.
{
"mcpServers": {
"cyanheads-pubchem-mcp-server": {
"url": "https://pubchem-mcp-server--cyanheads.run.tools"
}
}
}
Paste into .vscode/mcp.json.
{
"mcpServers": {
"cyanheads-pubchem-mcp-server": {
"url": "https://pubchem-mcp-server--cyanheads.run.tools"
}
}
}
Settings → Connectors → Add → Custom → Web. Paste the URL. Enable in a new chat.
Claude → Settings → Connectors → Add → Custom → Web
Name: pubchem-mcp-server
URL: https://pubchem-mcp-server--cyanheads.run.tools
OAuth only if this server requires it.
Save, start a new chat, enable the connector.
Developer mode custom connector. ChatGPT cannot reach localhost.
Settings → Apps & Connectors → Advanced → Developer mode ON
Create custom connector
Name: pubchem-mcp-server
MCP server URL: https://pubchem-mcp-server--cyanheads.run.tools
Auth: none unless the server requires OAuth
New chat → + → Developer mode → enable the connector
Register the HTTPS URL, then claude mcp list.
claude mcp add --transport http cyanheads-pubchem-mcp-server \
https://pubchem-mcp-server--cyanheads.run.tools
Pass on session/new as mcpServers when the agent advertised HTTP MCP.
[
{
"type": "http",
"name": "cyanheads-pubchem-mcp-server",
"url": "https://pubchem-mcp-server--cyanheads.run.tools"
}
]
Paste into a README or docs site. The widget loads snippets from Influzer — still not a SAFE badge.
Same handshake clock as this listing (overlay / warm / seed; live tools/list only if that is missing). Indigo is live_ok, amber is auth_required, gray is unreachable. Not a SAFE badge. Stdio listings have no badge.
[](https://www.influzer.ai/mcp/probe?url=https%3A%2F%2Fpubchem-mcp-server--cyanheads.run.tools)
<div data-influzer-install="cyanheads-pubchem-mcp-server"></div>
<script async src="https://www.influzer.ai/embed/install.js"></script>
https://www.influzer.ai/embed/mcp/cyanheads-pubchem-mcp-server.md
JSON: https://www.influzer.ai/api/v1/install/cyanheads-pubchem-mcp-server
Recipes using this server
No published recipes yet for this server.
Listing quality
Observable facts from our catalog and daily probe — not a safe-to-install badge.
- Surface
- Ready surface
- Auth gate
- Auth gate
- Tools source
- tools/list (live)
Observable catalog + probe facts — not a safe-to-install badge. How we verify.
Verification summary
Stored signals only. Not a safety score.
- Verification grade
- A (85)
- Last verified
- Status
- Auth required
- Response time
- 0 ms
- Auth
- Auth gate
- Transport
- http, HTTPS
- Tools indexed
- 10
- 30-day uptime
- 100% of 7 samples over 7 days
Probe history
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
Tools
(10)-
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. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.
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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), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.
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pubchem_get_compound_imageFetch a 2D structure diagram (PNG image) for a compound by CID.
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pubchem_get_compound_3d_structureGet a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns parsed atoms and bonds the model can reason over directly; 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).
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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 capped per type with total counts reported.
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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.
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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?".
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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. Richest for approved drugs; many compounds have no deposited interaction records.
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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 assay IDs (AIDs) which can be explored further with pubchem_get_summary.
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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.
Tool source: tools/list (live) · last probed 2026-11-05