pubchem-mcp-server

Server Details

MCP server for PubChem. Search compounds, properties, safety, bioactivity, xrefs, and summaries.

Status: Healthy
Last Tested: 2026-03-28 17:30
Transport: Streamable HTTP
URL
Repository: cyanheads/pubchem-mcp-server
GitHub Stars: 8
Server Listing: PubChem MCP Server

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Available Tools

8 tools

pubchem_get_bioactivityInspect

Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target information (gene symbols, protein names), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome to focus on active results.

ParametersJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID.
`maxResults`	No	Max assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20.
`outcomeFilter`	No	Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".	all

pubchem_get_compound_detailsInspect

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), 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.

ParametersJSON Schema

Name	Required	Description
`cids`	Yes	PubChem Compound IDs to fetch (1-100). Batched efficiently.
`properties`	No	Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity.
`includeSynonyms`	No	Fetch all known names and synonyms (trade names, systematic names, registry numbers).
`includeDescription`	No	Fetch textual description from PUG View (pharmacology, mechanism, therapeutic use). Adds one API call per CID — consider limiting CID count when enabled.
`includeDrugLikeness`	No	Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties.
`includeClassification`	No	Fetch pharmacological classification from PUG View: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Adds one API call per CID — consider limiting CID count when enabled.

pubchem_get_compound_imageInspect

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

ParametersJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID.
`size`	No	Image size: "small" (100x100) or "large" (300x300). Default: "large".	large

pubchem_get_compound_safetyInspect

Get GHS (Globally Harmonized System) hazard classification and safety data for a compound. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes). Data sourced from PubChem depositors — source attribution included.

ParametersJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID.

pubchem_get_compound_xrefsInspect

Get 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.

ParametersJSON Schema

Name	Required	Description
`cid`	Yes	PubChem Compound ID.
`xrefTypes`	Yes	Cross-reference types to retrieve. Options: RegistryID, RN (CAS numbers), PubMedID, PatentID, GeneID, ProteinGI, TaxonomyID.
`maxPerType`	No	Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references — this cap prevents bloat. Total count always reported. Default: 50.

pubchem_get_summaryInspect

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.

ParametersJSON Schema

Name	Required	Description	Default
`entityType`	Yes	Entity type. Determines ID format and returned fields.
`identifiers`	Yes	Entity identifiers (1-10). Type depends on entityType: - assay: AID (number), e.g. [1000] - gene: Gene ID (number), e.g. [1956] - protein: UniProt accession (string), e.g. ["P00533"] - taxonomy: Tax ID (number), e.g. [9606]

pubchem_search_assaysInspect

Find 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.

ParametersJSON Schema

Name	Required	Description
`maxResults`	No	Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.
`targetType`	Yes	Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions.
`targetQuery`	Yes	Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession).

pubchem_search_compoundsInspect

Search PubChem for chemical compounds. Five search modes:

identifier: Resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)
formula: Find compounds by molecular formula (Hill notation, e.g. "C6H12O6")
substructure: Find compounds containing a substructure (SMILES or CID)
superstructure: Find compounds that are substructures of the query
similarity: Find structurally similar compounds by 2D Tanimoto similarity

Optionally hydrate results with properties to avoid a follow-up details call.

ParametersJSON Schema

Name	Required	Description
`query`	No	Required for substructure/superstructure/similarity searches. A SMILES string or PubChem CID (as string) for the query structure.
`formula`	No	Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2").
`queryType`	No	Required for structure/similarity searches. Format of the query: "smiles" or "cid".
`threshold`	No	Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.
`maxResults`	No	Maximum CIDs to return (1-200). Default: 20.
`properties`	No	Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].
`searchType`	Yes	Search strategy: "identifier" (name/SMILES/InChIKey lookup), "formula", "substructure", "superstructure", or "similarity".
`identifiers`	No	Required for identifier search. Array of identifiers to resolve (1-25). Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES.
`identifierType`	No	Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey".
`allowOtherElements`	No	Formula search only. When true, includes compounds with additional elements beyond the formula.

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Claim this connector by publishing a /.well-known/glama.json file on your server's domain with the following structure:

{
  "$schema": "https://glama.ai/mcp/schemas/connector.json",
  "maintainers": [
    {
      "email": "your-email@example.com"
    }
  ]
}

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