io.github.cyanheads/pubchem-mcp-server

Official10 toolsLive

by cyanheads · TypeScript

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

The io.github.cyanheads/pubchem-mcp-server is an MCP server that searches the PubChem chemical database for compounds, properties, safety data, bioactivity, and cross-references. It provides entity summaries via MCP and supports STDIO or Streamable HTTP for tool access. The repository includes 10 tools and 6 resources.

🛠️ Key Features

PubChem compound search
Properties retrieval
Safety data access
Bioactivity lookup
Cross-references and entity summaries
MCP integration (STDIO or Streamable HTTP)

🚀 Use Cases

Cheminformatics workflows that need PubChem compound data
Safety- and bioactivity-oriented compound review
Linking PubChem records through cross-references

⚡ Developer Benefits

Tool-oriented MCP interface (10 tools)
Compatible transport options: STDIO or Streamable HTTP
Focused topic coverage: bioinformatics, cheminformatics, chemistry, and MCP

⚠️ Limitations

Available capabilities are limited to what the server exposes for PubChem search (10 tools); no additional data sources are indicated.

Topics

bioinformaticscheminformaticschemistryllm-toolsmcpmcp-serverpubchemscientific-computingcyanheads

Captured live from the server via tools/list.

pubchem_search_compounds

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.

Parameters11

searchType	string	required	Search strategy. "identifier": name/SMILES/InChIKey lookup. "formula": molecular formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query.
identifierType	string	optional	Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey".
identifiers	array	optional	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, ["BSYNRYMUTXBXSQ-UHFFFAOYSA-N"] for inchikey (27-char block format).
formula	string	optional	Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2").
allowOtherElements	boolean	optional	Formula search only. When true, includes compounds with additional elements beyond the formula.
query	string	optional	Required for substructure/superstructure/similarity searches. A SMILES string (e.g. "CC(=O)O") or PubChem CID as a string (e.g. "2244").
queryType	string	optional	Required for structure/similarity searches. Format of the query: "smiles" or "cid".
threshold	number	optional	Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.
offset	integer	optional	Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.
maxResults	integer	optional	Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20.
properties	array	optional	Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].

Raw schema

{
  "type": "object",
  "properties": {
    "searchType": {
      "type": "string",
      "enum": [
        "identifier",
        "formula",
        "substructure",
        "superstructure",
        "similarity"
      ],
      "description": "Search strategy. \"identifier\": name/SMILES/InChIKey lookup. \"formula\": molecular formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query."
    },
    "identifierType": {
      "description": "Required for identifier search. Type of chemical identifier: \"name\", \"smiles\", or \"inchikey\".",
      "type": "string",
      "enum": [
        "name",
        "smiles",
        "inchikey"
      ]
    },
    "identifiers": {
      "description": "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, [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format).",
      "minItems": 1,
      "maxItems": 25,
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "formula": {
      "description": "Required for formula search. Molecular formula in Hill notation (e.g. \"C6H12O6\", \"CaH2O2\").",
      "type": "string"
    },
    "allowOtherElements": {
      "default": false,
      "description": "Formula search only. When true, includes compounds with additional elements beyond the formula.",
      "type": "boolean"
    },
    "query": {
      "description": "Required for substructure/superstructure/similarity searches. A SMILES string (e.g. \"CC(=O)O\") or PubChem CID as a string (e.g. \"2244\").",
      "type": "string"
    },
    "queryType": {
      "description": "Required for structure/similarity searches. Format of the query: \"smiles\" or \"cid\".",
      "type": "string",
      "enum": [
        "smiles",
        "cid"
      ]
    },
    "threshold": {
      "default": 90,
      "description": "Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.",
      "type": "number",
      "minimum": 70,
      "maximum": 100
    },
    "offset": {
      "default": 0,
      "description": "Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 10000
    },
    "maxResults": {
      "default": 20,
      "description": "Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20.",
      "type": "integer",
      "minimum": 1,
      "maximum": 200
    },
    "properties": {
      "description": "Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. [\"MolecularFormula\", \"MolecularWeight\", \"CanonicalSMILES\"].",
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "MolecularFormula",
          "MolecularWeight",
          "CanonicalSMILES",
          "IsomericSMILES",
          "InChI",
          "InChIKey",
          "IUPACName",
          "Title",
          "XLogP",
          "ExactMass",
          "MonoisotopicMass",
          "TPSA",
          "Complexity",
          "Charge",
          "HBondDonorCount",
          "HBondAcceptorCount",
          "RotatableBondCount",
          "HeavyAtomCount",
          "IsotopeAtomCount",
          "AtomStereoCount",
          "DefinedAtomStereoCount",
          "UndefinedAtomStereoCount",
          "BondStereoCount",
          "DefinedBondStereoCount",
          "UndefinedBondStereoCount",
          "CovalentUnitCount",
          "Volume3D"
        ]
      }
    }
  },
  "required": [
    "searchType"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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). Accepts up to 100 CIDs per call.

Parameters10

cids	array	required	PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds.
properties	array	optional	Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity.
includeDescription	boolean	optional	Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions and are listed in the response's skippedCids.
descriptionOffset	integer	optional	Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous call to read the following page. Default: 0.
maxDescriptions	integer	optional	Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.
includeSynonyms	boolean	optional	Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists.
synonymOffset	integer	optional	Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read the following page. Default: 0.
maxSynonyms	integer	optional	Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20.
includeDrugLikeness	boolean	optional	Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency.
includeClassification	boolean	optional	Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification and are listed in the response's skippedCids.

Raw schema

{
  "type": "object",
  "properties": {
    "cids": {
      "minItems": 1,
      "maxItems": 100,
      "type": "array",
      "items": {
        "type": "integer",
        "exclusiveMinimum": 0,
        "maximum": 9007199254740991
      },
      "description": "PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds."
    },
    "properties": {
      "description": "Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity.",
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "MolecularFormula",
          "MolecularWeight",
          "CanonicalSMILES",
          "IsomericSMILES",
          "InChI",
          "InChIKey",
          "IUPACName",
          "Title",
          "XLogP",
          "ExactMass",
          "MonoisotopicMass",
          "TPSA",
          "Complexity",
          "Charge",
          "HBondDonorCount",
          "HBondAcceptorCount",
          "RotatableBondCount",
          "HeavyAtomCount",
          "IsotopeAtomCount",
          "AtomStereoCount",
          "DefinedAtomStereoCount",
          "UndefinedAtomStereoCount",
          "BondStereoCount",
          "DefinedBondStereoCount",
          "UndefinedBondStereoCount",
          "CovalentUnitCount",
          "Volume3D"
        ]
      }
    },
    "includeDescription": {
      "default": false,
      "description": "Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions and are listed in the response's skippedCids.",
      "type": "boolean"
    },
    "descriptionOffset": {
      "default": 0,
      "description": "Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous call to read the following page. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "maxDescriptions": {
      "default": 3,
      "description": "Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.",
      "type": "integer",
      "minimum": 1,
      "maximum": 20
    },
    "includeSynonyms": {
      "default": false,
      "description": "Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists.",
      "type": "boolean"
    },
    "synonymOffset": {
      "default": 0,
      "description": "Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read the following page. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "maxSynonyms": {
      "default": 20,
      "description": "Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20.",
      "type": "integer",
      "minimum": 1,
      "maximum": 100
    },
    "includeDrugLikeness": {
      "default": false,
      "description": "Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency.",
      "type": "boolean"
    },
    "includeClassification": {
      "default": false,
      "description": "Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification and are listed in the response's skippedCids.",
      "type": "boolean"
    }
  },
  "required": [
    "cids"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

pubchem_get_compound_image

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

Parameters2

cid	integer	required	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
size	string	optional	Image size: "small" (100x100) or "large" (300x300). Default: "large".

Raw schema

{
  "type": "object",
  "properties": {
    "cid": {
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    },
    "size": {
      "default": "large",
      "description": "Image size: \"small\" (100x100) or \"large\" (300x300). Default: \"large\".",
      "type": "string",
      "enum": [
        "small",
        "large"
      ]
    }
  },
  "required": [
    "cid"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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).

Parameters6

cid	integer	required	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
format	string	optional	Output format. "json" (default) returns parsed atoms and bonds. "sdf" returns the raw V2000 SDF text for passthrough to other tools.
includeAlternateConformerIds	boolean	optional	List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false.
maxAtoms	integer	optional	Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.
maxBonds	integer	optional	Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.
includeRawSdf	boolean	optional	For format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json".

Raw schema

{
  "type": "object",
  "properties": {
    "cid": {
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    },
    "format": {
      "default": "json",
      "description": "Output format. \"json\" (default) returns parsed atoms and bonds. \"sdf\" returns the raw V2000 SDF text for passthrough to other tools.",
      "type": "string",
      "enum": [
        "sdf",
        "json"
      ]
    },
    "includeAlternateConformerIds": {
      "default": false,
      "description": "List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false.",
      "type": "boolean"
    },
    "maxAtoms": {
      "description": "Cap the atoms returned in the format=\"json\" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "maxBonds": {
      "description": "Cap the bonds returned in the format=\"json\" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "includeRawSdf": {
      "default": false,
      "description": "For format=\"sdf\", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format=\"json\".",
      "type": "boolean"
    }
  },
  "required": [
    "cid"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

pubchem_get_compound_xrefs

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.

Parameters4

cid	integer	required	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
xrefTypes	array	required	Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID.
offset	integer	optional	Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0.
maxPerType	integer	optional	Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50.

Raw schema

{
  "type": "object",
  "properties": {
    "cid": {
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    },
    "xrefTypes": {
      "minItems": 1,
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "RegistryID",
          "RN",
          "PubMedID",
          "PatentID",
          "GeneID",
          "ProteinGI",
          "TaxonomyID"
        ]
      },
      "description": "Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID."
    },
    "offset": {
      "default": 0,
      "description": "Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "maxPerType": {
      "default": 50,
      "description": "Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50.",
      "type": "integer",
      "minimum": 1,
      "maximum": 500
    }
  },
  "required": [
    "cid",
    "xrefTypes"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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. Data sourced from PubChem depositors — source attribution included.

Parameters1

cids

array

required

PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.

Raw schema

{
  "type": "object",
  "properties": {
    "cids": {
      "minItems": 1,
      "maxItems": 25,
      "type": "array",
      "items": {
        "type": "integer",
        "exclusiveMinimum": 0,
        "maximum": 9007199254740991
      },
      "description": "PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds."
    }
  },
  "required": [
    "cids"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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), 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?".

Parameters6

cid	integer	required	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
outcomeFilter	string	optional	Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".
targetGeneId	integer	optional	Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this compound active against target T?".
targetAccession	string	optional	Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.
offset	integer	optional	Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.
maxResults	integer	optional	Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.

Raw schema

{
  "type": "object",
  "properties": {
    "cid": {
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    },
    "outcomeFilter": {
      "default": "all",
      "description": "Filter by activity outcome. \"active\" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: \"all\".",
      "type": "string",
      "enum": [
        "active",
        "inactive",
        "all"
      ]
    },
    "targetGeneId": {
      "description": "Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter=\"active\" to answer \"is this compound active against target T?\".",
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991
    },
    "targetAccession": {
      "description": "Filter to assays against this target protein accession (UniProt/GenBank), e.g. \"P35354\". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.",
      "type": "string"
    },
    "offset": {
      "default": 0,
      "description": "Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "maxResults": {
      "default": 20,
      "description": "Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.",
      "type": "integer",
      "minimum": 1,
      "maximum": 100
    }
  },
  "required": [
    "cid"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

pubchem_get_compound_interactions

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.

Parameters4

cid	integer	required	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
kinds	array	optional	Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"].
offset	integer	optional	Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.
maxEntries	integer	optional	Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10.

Raw schema

{
  "type": "object",
  "properties": {
    "cid": {
      "type": "integer",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    },
    "kinds": {
      "default": [
        "drug-drug"
      ],
      "description": "Interaction kinds to fetch. \"drug-drug\" (interactions with other drugs), \"drug-food\" (dietary interactions), \"target\" (binding/activity against molecular targets). Default: [\"drug-drug\"].",
      "minItems": 1,
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "drug-drug",
          "drug-food",
          "target"
        ]
      }
    },
    "offset": {
      "default": 0,
      "description": "Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 2147483646
    },
    "maxEntries": {
      "default": 10,
      "description": "Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10.",
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    }
  },
  "required": [
    "cid"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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.

Parameters4

targetType	string	required	Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions.
targetQuery	string	required	Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession).
offset	integer	optional	Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.
maxResults	integer	optional	Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.

Raw schema

{
  "type": "object",
  "properties": {
    "targetType": {
      "type": "string",
      "enum": [
        "genesymbol",
        "proteinname",
        "geneid",
        "proteinaccession"
      ],
      "description": "Target identifier type. \"genesymbol\" and \"proteinname\" accept text names. \"geneid\" accepts NCBI Gene IDs. \"proteinaccession\" accepts UniProt accessions."
    },
    "targetQuery": {
      "type": "string",
      "description": "Target identifier. Examples: \"EGFR\" (genesymbol), \"Epidermal growth factor receptor\" (proteinname), \"1956\" (geneid), \"P00533\" (proteinaccession)."
    },
    "offset": {
      "default": 0,
      "description": "Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "maxResults": {
      "default": 50,
      "description": "Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.",
      "type": "integer",
      "minimum": 1,
      "maximum": 200
    }
  },
  "required": [
    "targetType",
    "targetQuery"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

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.

Parameters2

entityType	string	required	Entity type. Determines ID format and returned fields.
identifiers	array	required	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]

Raw schema

{
  "type": "object",
  "properties": {
    "entityType": {
      "type": "string",
      "enum": [
        "assay",
        "gene",
        "protein",
        "taxonomy"
      ],
      "description": "Entity type. Determines ID format and returned fields."
    },
    "identifiers": {
      "minItems": 1,
      "maxItems": 10,
      "type": "array",
      "items": {
        "anyOf": [
          {
            "type": "string",
            "description": "String identifier (e.g. UniProt accession)."
          },
          {
            "type": "number",
            "description": "Numeric identifier (e.g. AID, Gene ID, Tax ID)."
          }
        ],
        "description": "Entity identifier — string or number depending on entityType."
      },
      "description": "Entity identifiers (1-10). Type depends on entityType:\n- assay: AID (number), e.g. [1000]\n- gene: Gene ID (number), e.g. [1956]\n- protein: UniProt accession (string), e.g. [\"P00533\"]\n- taxonomy: Tax ID (number), e.g. [9606]"
    }
  },
  "required": [
    "entityType",
    "identifiers"
  ],
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false
}

README.md19 KBView on GitHub

@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

Version MCP SDK TypeScript Bun

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

Overview

Chemical compound and bioassay data from PubChem's PUG REST and PUG View APIs. Search compounds by identifier, formula, or structure; fetch physicochemical properties, safety data, bioactivity, interactions, cross-references, and 3D structures; find bioassays by biological target. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.

Tools

Tool	Description
`pubchem_search_compounds`	Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.
`pubchem_get_compound_details`	Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.
`pubchem_get_compound_image`	Fetch a 2D structure diagram (PNG) for a compound by CID.
`pubchem_get_compound_3d_structure`	Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.
`pubchem_get_compound_xrefs`	Get external database cross-references (PubMed, patents, genes, proteins, etc.).
`pubchem_get_compound_safety`	Get GHS hazard classification and safety data for one or more compounds by CID (batch).
`pubchem_get_bioactivity`	Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.
`pubchem_get_compound_interactions`	Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.
`pubchem_search_assays`	Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).
`pubchem_get_summary`	Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

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.

Resource	Description
`pubchem://compound/{cid}`	Core physicochemical properties (JSON).
`pubchem://compound/{cid}/safety`	GHS hazard classification (JSON).
`pubchem://compound/{cid}/image`	2D structure diagram (PNG).
`pubchem://compound/{cid}/xrefs`	External cross-references (JSON).
`pubchem://compound/{cid}/bioactivity`	Bioassay activity profile (JSON).
`pubchem://assay/{aid}`	BioAssay summary (JSON).

Capability reference

`pubchem_search_compounds` _tool

Five search strategies: identifier (name/SMILES/InChIKey, batched 1-25), formula (Hill notation, optional allowOtherElements), substructure/superstructure containment, or 2D Tanimoto similarity (threshold 70-100, default 90)
Each strategy needs its own fields — identifier: identifierType + identifiers; formula: formula; substructure/superstructure/similarity: query + queryType — and a missing or blank one is rejected before the upstream call
Caps at 200 CIDs per page (default 20); offset pages to a ceiling of 10,000 — identifier lookups resolve every match up front so paging is free, while formula/structure/similarity searches cost more upstream per deep page
Optional properties hydration avoids a follow-up pubchem_get_compound_details call
Identifier mode reports unresolvedIdentifiers for inputs that resolved to no CID — no PubChem match, or a SMILES PubChem cannot interpret — while the rest of the batch still resolves, plus notices when multiple inputs collide on one CID
A query PubChem cannot search on (malformed SMILES or formula, a * wildcard atom, a CID with no record) fails fast with a search_query_rejected hint naming what to fix
Reports an exact totalFound when the full match set was observed, or a totalFoundAtLeast floor when a bounded upstream search saturated

`pubchem_get_compound_details` _tool

Up to 100 CIDs per call; 27 available properties, defaulting to a core set of 14 (formula, weight, IUPAC name, SMILES forms, InChIKey, XLogP, TPSA, H-bond/rotatable-bond counts, heavy atom count, charge, complexity)
Optional textual descriptions, paged via descriptionOffset/maxDescriptions (default 3, up to 20) — fetched only for the first 10 CIDs in the batch, remaining CIDs listed in skippedCids
Optional synonyms for every found CID, paged via synonymOffset/maxSynonyms (default 20, up to 100)
Optional drug-likeness assessment (Lipinski Rule of Five + Veber rules), computed from the returned properties at no extra latency
Optional pharmacological classification (FDA classes/mechanisms, MeSH classes, ATC codes) — same 10-CID fan-out cap as descriptions
Per-CID found: false distinguishes a nonexistent CID from a real compound PubChem simply has no data for

`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 — string IDs (RegistryID, RN for CAS numbers, PatentID) and numeric IDs (PubMedID, GeneID, ProteinGI, TaxonomyID)
Paged per type: maxPerType up to 500 (default 50), with the same offset applied across every requested type
Each type reports its own totalAvailable and truncated flag
Empty-result notice distinguishes "this compound has none of the requested types" from a possibly-mistyped CID

`pubchem_get_compound_safety` _tool

Batch of 1-25 CIDs
Returns GHS signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes), with source attribution
Per-CID status: ok, no_ghs_data (compound exists, no deposited classification), or cid_not_found (no PubChem record at all) — kept distinct so a bad CID never reads as "no hazards on file"
Precautionary statements carry a decoded flag — false for codes needing label-specific fill text or outside the decoder table; the code itself is still authoritative

`pubchem_get_bioactivity` _tool

Single CID; filter by outcomeFilter (active/inactive/all, default all) and/or targetGeneId/targetAccession
Caps at 100 results per page (default 20); offset reaches the rest
Reports totalAssays/activeCount/inactiveCount for the whole compound, plus filteredCount/returnedCount for the current page
Notices distinguish "no bioactivity data at all" from "the filter excluded everything" from "offset past the end"

`pubchem_get_compound_interactions` _tool

Single CID; one or more kinds — drug-drug (DrugBank), drug-food, target (binding/activity from BindingDB, ChEMBL, and others); default ["drug-drug"]
maxEntries per kind per page (1-50, default 10); offset counts source records rather than returned entries, capped at 2,147,483,646
Each kind pages independently — paging[] reports per-kind totalRecords/nextOffset/truncated; the top-level nextOffset is populated only when exactly one requested kind still has records left
A kind that fails to retrieve is named in failedKinds without failing the kinds that succeeded

`pubchem_search_assays` _tool

Search by targetType: genesymbol/proteinname (text), geneid (NCBI Gene ID), proteinaccession (UniProt)
Caps at 200 AIDs per page (default 50); offset pages to the total found
Rejects a blank targetQuery and a non-numeric geneid query before the upstream call
Reports totalFound across all pages and distinguishes "no match" from "offset past the end"

`pubchem_get_summary` _tool

entityType: assay (AID), gene (NCBI Gene ID), protein (UniProt accession), or taxonomy (Tax ID); up to 10 identifiers per call
Per-identifier found flag; populated fields depend on entityType (taxonomy includes an ordered lineage, gene includes symbol/taxonomy)
Notice reports how many identifiers were not found and which ID type entityType expects

`pubchem://compound/{cid}` _resource

Core physicochemical properties (the same default 14-property set as pubchem_get_compound_details), as application/json
Throws a typed not-found when the CID doesn't exist in PubChem
Use pubchem_get_compound_details to select specific properties or add descriptions, synonyms, drug-likeness, and classification

`pubchem://compound/{cid}/safety` _resource

GHS hazard classification as application/json
status (ok/no_ghs_data/cid_not_found) is the only signal distinguishing a bad CID from a compound with no deposited classification — a resource read has no notice surface

`pubchem://compound/{cid}/image` _resource

2D structure diagram, 300x300 PNG, returned as a base64 blob
Use pubchem_get_compound_image for the 100x100 size option

`pubchem://compound/{cid}/xrefs` _resource

Focused default set — RN (CAS), RegistryID, PubMedID — up to 25 IDs per type, as application/json
Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and offset paging

`pubchem://compound/{cid}/bioactivity` _resource

Up to 25 assays as application/json, plus totalAssays/activeCount for the whole compound
Use pubchem_get_bioactivity to filter by outcome or target, raise the cap, or page with offset

`pubchem://assay/{aid}` _resource

BioAssay summary as application/json — name, description, source, protocol, substance counts
Throws a typed not-found when the AID doesn't exist

Features

Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.

PubChem-specific:

Covers both PUG REST (search, properties, cross-references, safety, bioactivity, interactions) and PUG View (textual descriptions, pharmacological classification) endpoints
Rate-limited client (5 req/s) with automatic request queuing, and retry with exponential backoff on 5xx errors and network failures
A cancelled tool call or resource read stops its PubChem work — queued requests, in-flight fetches, retry backoffs, and async-search polling — and fails with RequestCancelled
Hand-rolled V2000 SDF parser for 3D conformer atoms and bonds; drug-likeness (Lipinski/Veber) computed from already-fetched properties, adding no extra latency
All tools are read-only and idempotent — no API keys required, PubChem's API is freely accessible

Agent-friendly output:

Discriminated output contracts — per-CID status (ok / no_ghs_data / cid_not_found) and found flags let callers branch on data instead of matching an error string
Graceful partial failure — batch tools return per-item results alongside unresolvedIdentifiers, skippedCids, and failedKinds rather than failing the whole call
Response shaping — truncation disclosure (truncated, shown/cap, nextOffset) on every capped list, plus a totalFoundAtLeast floor in place of a count when an upstream search saturates
Typed error reasons — validation and not-found failures declare a reason (e.g. cid_not_found, missing_identifier_args, invalid_cid_query) with actionable recovery text, not generic messages

Getting started

Public Hosted Instance

A public instance is available at https://pubchem.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "streamable-http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add the following to your MCP client configuration file.

json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/pubchem-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

Or with npx (no Bun required):

json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/pubchem-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

Or with Docker:

json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubchem-mcp-server:latest"]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

Prerequisites

Bun v1.4.0 or higher (or Node.js v24+).
No API keys required — PubChem's API is freely accessible.

Installation

Clone the repository:

git clone https://github.com/cyanheads/pubchem-mcp-server.git

Navigate into the directory:

cd pubchem-mcp-server

Install dependencies:

bun install

Configure environment (optional):

cp .env.example .env
# edit .env to override transport, session mode, storage, or logging defaults

Configuration

Variable	Description	Default
`MCP_TRANSPORT_TYPE`	Transport: `stdio` or `http`.	`stdio`
`MCP_HTTP_PORT`	Port for HTTP server.	`3010`
`MCP_HTTP_HOST`	Host for HTTP server.	`127.0.0.1`
`MCP_SESSION_MODE`	`stateless`, `stateful`, or `auto`. PubChem needs no multi-round-trip input, so the server declares `stateless`; the example and Docker set it to match.	`stateless`
`MCP_AUTH_MODE`	Auth mode: `none`, `jwt`, or `oauth`.	`none`
`MCP_LOG_LEVEL`	Log level (RFC 5424).	`info`
`STORAGE_PROVIDER_TYPE`	Storage backend.	`in-memory`
`OTEL_ENABLED`	Enable OpenTelemetry.	`false`

See .env.example for the full list of optional overrides.

Running the server

Local development

Build and run:

# One-time build
bun run rebuild

# Run the built server
bun run start:stdio
# or
bun run start:http

Run checks and tests:

bun run devcheck   # Lint, format, typecheck, security
bun run test       # Vitest test suite
bun run lint:mcp   # Validate MCP definitions against spec

Docker

docker build -t pubchem-mcp-server .
docker run --rm -p 3010:3010 pubchem-mcp-server

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/pubchem-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Directory	Purpose
`src/index.ts`	`createApp()` entry point — registers tools/resources and inits the PubChem client.
`src/mcp-server/tools/definitions/`	Tool definitions (`*.tool.ts`).
`src/mcp-server/resources/definitions/`	Resource definitions (`*.resource.ts`).
`src/services/pubchem/`	PubChem API client — rate limiting, retry, and response/SDF parsing.
`scripts/`	Build, clean, devcheck, and tree generation scripts.
`tests/`	Unit and integration tests.

Development guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

Handlers throw, framework catches — no try/catch in tool logic
Use ctx.log for request-scoped logging
Wrap external API calls: validate the raw PubChem response → normalize to a domain type → return the output schema; never fabricate missing fields
Register new tools and resources in the index.ts barrel files

Contributing

Issues are welcome. Run checks before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.

Install

Tools (10)

pubchem_search_compoundspubchem_get_compound_detailspubchem_get_compound_imagepubchem_get_compound_3d_structurepubchem_get_compound_xrefspubchem_get_compound_safetypubchem_get_bioactivitypubchem_get_compound_interactions

Configuration

Environment variables

MCP_LOG_LEVELdefault info

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

MCP_SESSION_MODEdefault stateless

HTTP session mode: stateless, stateful, or auto. Stateless is sufficient for PubChem; auto resolves to stateful.

MCP_HTTP_HOSTdefault 127.0.0.1

The hostname for the HTTP server.

MCP_HTTP_PORTdefault 3010

The port to run the HTTP server on.

MCP_HTTP_ENDPOINT_PATHdefault /mcp

The endpoint path for the MCP server.

MCP_AUTH_MODEdefault none

Authentication mode to use: 'none', 'jwt', or 'oauth'.

Add to VS Code Add to Cursor

claude_desktop_config.json

json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server@0.6.5",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

🛠️ Key Features

🚀 Use Cases

⚡ Developer Benefits

⚠️ Limitations

Topics

pubchem_search_compounds

pubchem_get_compound_details

pubchem_get_compound_image

pubchem_get_compound_3d_structure

pubchem_get_compound_xrefs

pubchem_get_compound_safety

pubchem_get_bioactivity

pubchem_get_compound_interactions

pubchem_search_assays

pubchem_get_summary

@cyanheads/pubchem-mcp-server

Overview

Tools

Resources

Capability reference

pubchem_search_compounds tool

pubchem_get_compound_details tool

pubchem_get_compound_image tool

pubchem_get_compound_3d_structure tool

pubchem_get_compound_xrefs tool

pubchem_get_compound_safety tool

pubchem_get_bioactivity tool

pubchem_get_compound_interactions tool

pubchem_search_assays tool

pubchem_get_summary tool

pubchem://compound/{cid} resource

pubchem://compound/{cid}/safety resource

pubchem://compound/{cid}/image resource

pubchem://compound/{cid}/xrefs resource

pubchem://compound/{cid}/bioactivity resource

pubchem://assay/{aid} resource

Features

Getting started

Public Hosted Instance

Self-Hosted / Local

Prerequisites

Installation

Configuration

Running the server

Local development

Docker

Project structure

Development guide

Contributing

License

Install

Configuration

Related servers

`pubchem_search_compounds` _tool

`pubchem_get_compound_details` _tool

`pubchem_get_compound_image` _tool

`pubchem_get_compound_3d_structure` _tool

`pubchem_get_compound_xrefs` _tool

`pubchem_get_compound_safety` _tool

`pubchem_get_bioactivity` _tool

`pubchem_get_compound_interactions` _tool

`pubchem_search_assays` _tool

`pubchem_get_summary` _tool

`pubchem://compound/{cid}` _resource

`pubchem://compound/{cid}/safety` _resource

`pubchem://compound/{cid}/image` _resource

`pubchem://compound/{cid}/xrefs` _resource

`pubchem://compound/{cid}/bioactivity` _resource

`pubchem://assay/{aid}` _resource