Pubchem MCP server

• pubchem_get_bioactivityFree

  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 accession) to focus the profile — e.g. "is this compound active against target T?".

• pubchem_get_compound_3d_structureFree

  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).

• pubchem_get_compound_detailsFree

  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). Accepts up to 100 CIDs per call.

• pubchem_get_compound_imageFree

  Fetch a 2D structure diagram (PNG image) for a compound by CID.

• pubchem_get_compound_interactionsFree

  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 offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.

• pubchem_get_compound_safetyFree

  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 from PubChem depositors — source attribution included.

• pubchem_get_compound_xrefsFree

  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.

• pubchem_get_summaryFree

  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.

• pubchem_search_assaysFree

  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_search_compoundsFree

  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 matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.

• Code scan49 source files scanned; 49 source files scanned25/25
• Live reliabilityremote reachable in 987ms20/20
• Tool poisoning10 tool descriptions checked15/15
• Auth qualityopen endpoint, read-only tools10/15
• Maintenancelast push 0 days ago15/15
• Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10

Pubchem: common questions

Is Pubchem MCP server safe?

Yes, by our scan: it is graded A (93/100). Read the Pubchem safety report

How do I install Pubchem?

It runs remotely at pubchem.caseyjhand.com. Add it to Claude Code, Claude Desktop or Cursor with the snippets above, or call it through the mcp.market gateway without installing anything.

Does Pubchem need an API key?

No secret keys are declared. It reads 7 settings from the environment.

Is Pubchem maintained?

The last commit was in the last day (2026-09-19). The latest release is v0.6.3.

Is Pubchem up?

100% of our last 4 checks got an answer. We check remote servers about four times a day.

What can I use instead of Pubchem?

Servers from other publishers that do the same job: AI Pensieve MCP server, CiteNexus MCP server and CLI MCP server. Compare all Pubchem alternatives.