pubchem-mcp-server

io.github.cyanheads/pubchem-mcp-serverVersion 0.8.1

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

Status

Responds288 msNov 14, 2026, 14:48 UTCAnswered our handshake without sign-in.

Registry data may be out of date

We could not refresh it, so this page shows the last copy.

Last checked: Nov 14, 2026, 14:48 UTC
Latency: 288 ms
Remotes responding: 1 of 1
Sign-in: No sign-in
Hosting: Hosted outside the EU (detected)
Registry data as of: Nov 14, 2026, 22:14 UTC

Data from the official MCP Registry, checked by run.zero. How we check

Connect

Streamable HTTP

https://pubchem.caseyjhand.com/mcpResponds288 msNov 14, 2026, 14:48 UTC

No sign-in

Claude Code

claude mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcp

Claude Desktop and claude.ai

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Settings > Connectors > Add custom connector
Name: pubchem-mcp-server
Remote MCP server URL: https://pubchem.caseyjhand.com/mcp

Cursor

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

VS Code

code --add-mcp '{"name":"pubchem-mcp-server","type":"http","url":"https://pubchem.caseyjhand.com/mcp"}'

Streamable HTTP

npm: @cyanheads/pubchem-mcp-server 0.8.1

Package only

npm (npx)

claude mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server@0.8.1

Streamable HTTP

npm: @cyanheads/pubchem-mcp-server 0.8.1

Package only

npm (npx)

claude mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server@0.8.1

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Tools

10 tools

Tools of pubchem-mcp-server
	Description		Read-only	Idempotent	Open world
`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), quantitative values (IC50, EC50, Ki, etc.), each assay's type (confirmatory, screening, summary, other), and the PubMed IDs it cites. Filter by outcome, a specific molecular target (NCBI Gene ID or protein accession), and/or assay type to focus the profile — e.g. "is this compound active against target T in confirmatory assays?".	Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), quantitative values (IC50, EC50, Ki, etc.), each assay's type (confirmatory, screening, summary, other), and the PubMed IDs it cites. Filter by outcome, a specific molecular target (NCBI Gene ID or protein accession), and/or assay type to focus the profile — e.g. "is this compound active against target T in confirmatory assays?".	Not declared	Yes	Yes	Yes
`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 conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).	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 conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).	Not declared	Yes	Yes	Yes
`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 pharmacological classification (FDA classes, MeSH classes, ATC codes). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.	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 pharmacological classification (FDA classes, MeSH classes, ATC codes). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.	Not declared	Yes	Yes	Yes
`pubchem_get_compound_image`Fetch a 2D structure diagram (PNG image) for a compound by CID.	Fetch a 2D structure diagram (PNG image) for a compound by CID.	Not declared	Yes	Yes	Yes
`pubchem_get_compound_interactions`Get a compound's interaction data: drug-food interactions, and the molecular targets its bioassays name — one entry per target as kinds defines it, with its assay counts by outcome and most potent active value, Active targets first, most potent first. Each entry carries its originating source. Results are paged per kind, with the record total and the next offset reported for each. Drug-food coverage is richest for approved drugs; target covers any compound PubChem has assay data for, and pubchem_get_bioactivity lists one target's assays when given the entry's GeneID or accession. Drug-drug interactions (DrugBank) are unavailable while PubChem's SDQ service refuses automated requests: an explicit drug-drug request is reported in failedKinds while the other kinds still return.	Get a compound's interaction data: drug-food interactions, and the molecular targets its bioassays name — one entry per target as kinds defines it, with its assay counts by outcome and most potent active value, Active targets first, most potent first. Each entry carries its originating source. Results are paged per kind, with the record total and the next offset reported for each. Drug-food coverage is richest for approved drugs; target covers any compound PubChem has assay data for, and pubchem_get_bioactivity lists one target's assays when given the entry's GeneID or accession. Drug-drug interactions (DrugBank) are unavailable while PubChem's SDQ service refuses automated requests: an explicit drug-drug request is reported in failedKinds while the other kinds still return.	Not declared	Yes	Yes	Yes
`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 word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.	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 word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.	Not declared	Yes	Yes	Yes
`pubchem_get_compound_xrefs`Get external database cross-references for a compound: PubMed citations, patent IDs, gene associations, CAS and EC numbers with the number of source records that deposited each, other 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 recently assigned) first and the other numeric types in ascending order; CAS and EC come most-attested first; the other string IDs keep PubChem's order. A type that fails to load is named in failedTypes while the others still return; the call fails only when a type fails and no type other than ProteinGI (which PubChem no longer serves) loads.	Get external database cross-references for a compound: PubMed citations, patent IDs, gene associations, CAS and EC numbers with the number of source records that deposited each, other 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 recently assigned) first and the other numeric types in ascending order; CAS and EC come most-attested first; the other string IDs keep PubChem's order. A type that fails to load is named in failedTypes while the others still return; the call fails only when a type fails and no type other than ProteinGI (which PubChem no longer serves) loads.	Not declared	Yes	Yes	Yes
`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.	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.	Not declared	Yes	Yes	Yes
`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.	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.	Not declared	Yes	Yes	Yes
`pubchem_search_compounds`Search PubChem for chemical compounds by identifier (name, SMILES, InChI, 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 past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.	Search PubChem for chemical compounds by identifier (name, SMILES, InChI, 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 past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.	Not declared	Yes	Yes	Yes

Details

Registry status: Active
Published: Nov 11, 2026
Updated: Nov 11, 2026
Website: Not given
Repository: https://github.com/cyanheads/pubchem-mcp-server⁠ (opens in a new tab)
Categories (suggested): Design and mediaSuggested categories are assigned automatically from the registry text and may be wrong. Verified operators can correct them.
GDPR: Not declared

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