Pubchem MCP Server

@cyanheads/pubchem-mcp-server Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP. 10 Tools • 6 Resources • 1 Skill

Public Hosted Server: https://pubchem.caseyjhand.com/mcp

Overview

Chemical compounds and bioassays from PubChem. Search compounds by name, formula, or structure; fetch properties, safety data, bioactivity, drug-food interactions, molecular targets, and 3D structures; and find bioassays by biological target.

Tools

Resources

Compound and assay records are also exposed as URI-templated resources, backed by the same client methods as the tools; many MCP clients are tool-only and never surface resources.

Skills

The server publishes an agent skill, pubchem-guide, covering gates and identifier chains the tool descriptions don't carry: salt vs parent CIDs, where Gene IDs and accessions come from, why gene-symbol, Gene ID, and accession searches disagree, and how to read activity labels, potency values, and GHS data. Plugin installs (Claude Code, Codex) and the .mcpb bundle pick it up from skills/, and the server also serves it over MCP as skill://pubchem-guide/SKILL.md.

Capability reference

pubchem_search_compounds tool

• Six search strategies: identifier (identifierType + identifiers; name/SMILES/InChI/InChIKey, 25 per call, the rest returned in unprocessed), formula (formula, Hill notation, optional allowOtherElements), substructure/superstructure and 2D similarity (query + queryType; similarity threshold 70-100, default 90), or assay (aid; compounds the bioassay marked active, or every compound tested with activeOnly: false)
• Up to 200 CIDs per page (default 20; a larger maxResults is served at 200 and reported in cappedInputs); offset pages identifier and assay searches to the end of their matches, and formula, substructure, superstructure, and similarity searches to 10,000 (deeper fails with offset_ceiling_exceeded). Optional properties saves a follow-up pubchem_get_compound_details call
• Reports totalFound, or a totalFoundAtLeast floor when an upstream search saturated, and unresolvedIdentifiers for inputs with no CID. Fails with aid_not_found for an unknown AID and search_query_rejected (with a hint) for a query PubChem cannot search

pubchem_get_compound_details tool

• Up to 100 CIDs per call (the rest returned in unprocessed); 27 available properties, defaulting to a core set of 14
• Optional descriptions (descriptionOffset/maxDescriptions, default 3, max 20) and classification (FDA, MeSH, ATC) cover the first 10 CIDs only, the rest listed in skippedCids. Optional synonyms (synonymOffset/maxSynonyms, default 20, max 100) and a Lipinski/Veber drug-likeness check cover every found CID
• Per-CID found: false separates a nonexistent CID from a compound with no data

pubchem_get_compound_image tool

• Single CID; size is "small" (100x100) or "large" (300x300, default)
• Returns base64-encoded PNG plus width/height
• Typed cid_not_found error when PubChem has no record for the CID

pubchem_get_compound_3d_structure tool

• Single CID; format="json" (default) returns parsed atoms (element + x/y/z) and bonds, format="sdf" returns the raw V2000 SDF text
• maxAtoms/maxBonds cap the JSON preview (default 200 each); atomCount/bondCount always report the full totals, with any capping disclosed via enrichment
• includeRawSdf bypasses the default 500-line cap on the raw SDF text
• Optional includeAlternateConformerIds lists conformer IDs beyond the default
• Typed no_3d_structure error when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)

pubchem_get_compound_xrefs tool

• Single CID; one or more xrefTypes: CAS, EC, RN, RegistryID, PatentID, PubMedID, GeneID, ProteinGI, TaxonomyID
• CAS and EC are the numbers deposited for the compound, every distinct value ordered by how many source records deposited it, with those counts in sourceCounts. RN is PubChem's unranked registry-number list: the CAS number sits beside deprecated and related CAS RNs and EC numbers
• ProteinGI currently returns no data from PubChem; use GeneID for gene/protein associations
• maxPerType up to 500 (default 50), with one offset applied to every type; each type reports totalAvailable and truncated. PubMedID comes newest first
• A type that fails to load is named in failedTypes and the others still return; the call fails only when a type fails and no type other than ProteinGI (which PubChem no longer serves) loads. An empty result says whether the compound has none of the requested types or the CID may be mistyped

pubchem_get_compound_safety tool

• Up to 25 CIDs per call (the rest returned in unprocessed)
• Returns the GHS signal word, pictograms, H-codes, and P-codes merged across sources, plus classifications[] with each source's own label; precautionary statements carry a decoded flag
• Per-CID status: ok, not_classified (notifiers found no GHS hazard), no_ghs_data (no deposited classification), or cid_not_found, so a bad CID never reads as "no hazards on file"

pubchem_get_bioactivity tool

• Single CID; filter by outcomeFilter (active/inactive/all, default all), targetGeneId/targetAccession, and assayType (any of confirmatory/screening/summary/other); an assay must pass every filter set
• A target filter matches any identifier tied to the same target, so Gene ID 5742, UniProt P23219, and RefSeq NP_542158 all reach the same COX-1 assays
• Each result carries the assay's assayType and the PubMed IDs it cites (pmids, newest first)
• Up to 100 results per page (default 20); offset reaches the rest. A multi-target assay reports the matched target and lists the others under otherTargets
• Reports totalAssays/activeCount/inactiveCount for the whole compound and filteredCount/returnedCount for the page; notices say whether there is no data, the filter excluded everything, or offset is past the end

pubchem_get_compound_interactions tool

• Single CID; one or more kinds — drug-food (PUG View), target, drug-drug (DrugBank); default ["drug-food"], and an empty drug-food page points at target
• target gives one entry per target the compound's assay summary names: a Gene ID with the accessions the table pairs with it, or an identifier it never pairs. A Gene ID and an accession that no row pairs are separate entries even when they name the same protein (erlotinib's ERBB2 appears as accession:P04626 and as GeneID:2064). Each entry names the target from a batched gene or protein summary lookup, plus the GeneID: or accession: value pubchem_get_bioactivity filters on, and states the assay counts by outcome and the most potent Active value with its AID. Active targets come first, most potent first. If a name lookup fails or does not answer within a few seconds, the entries keep their identifier and the notice says so
• maxEntries per kind per page (max 50, default 10); offset counts records (targets, for target), up to 2,147,483,646. Each kind pages independently, reported in paging[] (totalRecords/nextOffset/truncated)
• A kind that fails is named in failedKinds and the others still return. The notice offers a retry only for a failure a retry can clear (timeout, rate limit, network error, unreadable response, 5xx other than 501); an HTTP 400, 403, or 501, or a response in a shape the server does not expect, fails the same way on every call. drug-drug comes from PubChem's SDQ service, which refuses automated requests, so it lands in failedKinds and a retry will not help