Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Scored across 10 tools
Most tools target clearly distinct resources/actions (search vs. details vs. 3D structure vs. image vs. safety vs. xrefs). The one real overlap is between pubchem_get_bioactivity (per-assay records) and pubchem_get_compound_interactions (per-target rollup), but the descriptions explicitly explain the relationship and point to each other, so an agent can choose correctly. pubchem_get_summary vs pubchem_get_compound_details is also a potential confusion point, resolved by the summary tool's explicit entity-type scoping.
All tools use the same pubchem_ prefix followed by a consistent verb_noun pattern (search_compounds, search_assays, get_compound_details, get_compound_safety, get_summary). Compound-scoped tools uniformly use get_compound_<aspect>, which makes the family structure obvious at a glance.
Ten tools is well within the sweet spot and each covers a distinct PubChem data domain (search, properties, 3D, image, safety, xrefs, bioactivity, interactions, assay lookup, entity summaries). No tool appears redundant or filler.
Compound and assay coverage is broad and includes search, hydration, paging, and cross-references, so core discovery-to-detail workflows have no dead ends. Minor gaps: there is no search tool for genes/proteins/taxonomy entities (only summary-by-ID), and assay exploration stops at pubchem_get_summary rather than a dedicated assay-details tool, forcing agents to already know the identifiers.
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?".
Inputs: cid (required), offset, assayType, maxResults, +3 more. Returns: cap, cid, error, shown, +14 more
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).
Inputs: cid (required), format, maxAtoms, maxBonds, +2 more. Returns: cid, sdf, atoms, bonds, +12 more
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.
Inputs: cids (required), properties, maxSynonyms, synonymOffset, +6 more. Returns: error, notice, compounds, truncated, +8 more
Fetch a 2D structure diagram (PNG image) for a compound by CID.
Inputs: cid (required), size. Returns: cid, error, width, height, +2 more
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.
Inputs: cid (required), kinds, offset, maxEntries. Returns: cid, error, notice, offset, +8 more
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.
Inputs: cids (required). Returns: error, notice, results, unprocessed, +3 more
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.
Inputs: cid (required), xrefTypes (required), offset, maxPerType. Returns: cid, error, xrefs, notice, +5 more
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.
Inputs: entityType (required), identifiers (required). Returns: error, notice, summaries, entityType, +4 more
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.
Inputs: targetType (required), targetQuery (required), offset, maxResults. Returns: cap, aids, error, shown, +8 more
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.
Inputs: searchType (required), aid, query, offset, +9 more. Returns: cap, error, shown, notice, +11 more
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
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