PubChem

name: PubChem
description: PubChem is NCBI's open chemistry database containing information on more than 100 million chemical compounds. It provides REST and view APIs for searching chemical structures, retrieving molecular properties, bioactivity data, safety information, and drug information. PubChem integrates data from hundreds of data sources and is freely accessible without authentication for standard use.
image: https://pubchem.ncbi.nlm.nih.gov/favicon.ico
tags:
  - Chemistry
  - Chemical Compounds
  - Drug Discovery
  - Bioassay
  - Life Sciences
  - NCBI
  - Bioinformatics
url: https://pubchem.ncbi.nlm.nih.gov/
created: "2026-06-13"
modified: "2026-06-13"
specificationVersion: "0.19"
apis:

  - name: PubChem PUG REST API
    description: The Power User Gateway (PUG) REST API provides programmatic access to PubChem compound, substance, and bioassay data. Supports lookup by name, CID, SID, InChI, SMILES, and structure search. Returns molecular properties, identifiers, 2D/3D structures, bioactivity summaries, cross-references, synonyms, and images.
    humanURL: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest
    baseURL: https://pubchem.ncbi.nlm.nih.gov/rest/pug
    tags:
      - Compounds
      - Substances
      - Bioassays
      - Structure Search
      - Chemical Properties
    properties:
      - type: Documentation
        url: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest
      - type: OpenAPI
        url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/openapi.json
    contact:
      - FN: PubChem Help Desk
        email: [email protected]
    operations:
      - summary: Get compound by CID
        method: GET
        path: /compound/cid/{cid}/JSON
        description: Retrieve full compound record by PubChem Compound ID (CID) in JSON format.
      - summary: Get compound by name
        method: GET
        path: /compound/name/{name}/JSON
        description: Retrieve compound records by chemical name, returning CID and full compound data.
      - summary: Get compound by SMILES
        method: GET
        path: /compound/smiles/{smiles}/JSON
        description: Retrieve compound records by canonical SMILES string.
      - summary: Get compound by InChI
        method: GET
        path: /compound/inchi/{inchi}/JSON
        description: Retrieve compound records by IUPAC International Chemical Identifier.
      - summary: Get compound properties
        method: GET
        path: /compound/cid/{cid}/property/{properties}/JSON
        description: Retrieve selected calculated properties (MolecularFormula, MolecularWeight, CanonicalSMILES, InChI, InChIKey, IUPACName, XLogP, TPSA, etc.) for a compound.
      - summary: Get compound synonyms
        method: GET
        path: /compound/cid/{cid}/synonyms/JSON
        description: Retrieve all synonyms and alternative names for a compound.
      - summary: Get compound SIDs
        method: GET
        path: /compound/cid/{cid}/sids/JSON
        description: Retrieve all substance IDs (SIDs) associated with a compound.
      - summary: Get compound cross-references
        method: GET
        path: /compound/cid/{cid}/xrefs/{xreftypes}/JSON
        description: Retrieve external cross-references (RegistryID, RN, PubMedID, MMDBID, ProteinGI, NucleotideGI, TaxonomyID, MIMID, GeneID, ProbeID, PatentID) for a compound.
      - summary: Get compound image
        method: GET
        path: /compound/cid/{cid}/PNG
        description: Retrieve a 2D structure image of a compound in PNG format.
      - summary: Get compound bioassay summary
        method: GET
        path: /compound/cid/{cid}/assaysummary/JSON
        description: Retrieve a summary of bioassay results for a compound, including activity outcomes and assay metadata.
      - summary: Substructure search
        method: GET
        path: /compound/substructure/smiles/{smiles}/JSON
        description: Search for compounds containing a specified substructure using SMILES, InChI, or SDF input. Returns async listkey for large result sets.
      - summary: Superstructure search
        method: GET
        path: /compound/superstructure/smiles/{smiles}/JSON
        description: Search for compounds that are superstructures of the specified structure.
      - summary: Similarity search
        method: GET
        path: /compound/fastsimilarity_2d/smiles/{smiles}/JSON
        description: Fast 2D Tanimoto similarity search for structurally similar compounds.
      - summary: Get substance by SID
        method: GET
        path: /substance/sid/{sid}/JSON
        description: Retrieve a substance record by PubChem Substance ID (SID), including source information, synonyms, and associated compound.
      - summary: Get substance synonyms
        method: GET
        path: /substance/sid/{sid}/synonyms/JSON
        description: Retrieve all synonyms for a substance record.
      - summary: Get assay by AID
        method: GET
        path: /assay/aid/{aid}/JSON
        description: Retrieve a full bioassay record by Assay ID (AID), including protocol, results schema, and experimental data.
      - summary: Get assay description
        method: GET
        path: /assay/aid/{aid}/description/JSON
        description: Retrieve descriptive metadata for a bioassay, including title, protocol, target information, and measurement parameters.
      - summary: Get assay results
        method: GET
        path: /assay/aid/{aid}/CSV
        description: Retrieve bioassay experimental results in CSV format with all tested substance outcomes and activity values.
      - summary: Retrieve async results by listkey
        method: GET
        path: /compound/listkey/{listkey}/cids/JSON
        description: Poll for and retrieve results from an asynchronous structure search query using the listkey returned during the search initiation.

  - name: PubChem PUG View API
    description: The PUG View API provides access to the full structured compound and substance pages as seen on the PubChem website, organized as hierarchical sections covering names, structures, physical and chemical properties, safety data, pharmacology, biological activities, toxicology, literature references, and more.
    humanURL: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view
    baseURL: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view
    tags:
      - Compound Data
      - Safety Data
      - Pharmacology
      - Toxicology
      - Structured Data
    properties:
      - type: Documentation
        url: https://pubchem.ncbi.nlm.nih.gov/docs/pug-view
    contact:
      - FN: PubChem Help Desk
        email: [email protected]
    operations:
      - summary: Get full compound data page
        method: GET
        path: /data/compound/{cid}/JSON
        description: Retrieve all structured data for a compound as seen on its PubChem compound page, organized in hierarchical sections.
      - summary: Get compound data section
        method: GET
        path: /data/compound/{cid}/JSON
        description: Retrieve a specific section of a compound data page using the heading parameter (e.g., Safety+and+Hazards, Pharmacology+and+Biochemistry, Chemical+and+Physical+Properties).
      - summary: Get full substance data page
        method: GET
        path: /data/substance/{sid}/JSON
        description: Retrieve all structured data for a substance record in hierarchical section format.
      - summary: Get annotations by heading
        method: GET
        path: /annotations/heading/{heading}/JSON
        description: Retrieve annotations across all compounds for a specific data heading (e.g., Boiling+Point, LogP, Melting+Point).
      - summary: Get data in XML format
        method: GET
        path: /data/compound/{cid}/XML
        description: Retrieve full compound structured data in XML format.
      - summary: Get data in ASNT format
        method: GET
        path: /data/compound/{cid}/ASNT
        description: Retrieve full compound structured data in ASN.1 text format for programmatic parsing.

  - name: PubChem PUG SOAP API
    description: Legacy SOAP/XML web service interface for PubChem providing structure search, identity search, and chemical standardization capabilities. Supports submitting queries and retrieving results in ASN.1, XML, and SDF formats.
    humanURL: https://pubchem.ncbi.nlm.nih.gov/pug/pugsoap.cgi?wsdl
    baseURL: https://pubchem.ncbi.nlm.nih.gov/pug/pugsoap.cgi
    tags:
      - SOAP
      - Legacy
      - Structure Search
      - Chemical Standardization
    properties:
      - type: Documentation
        url: https://pubchem.ncbi.nlm.nih.gov/docs/pug-soap
      - type: WSDL
        url: https://pubchem.ncbi.nlm.nih.gov/pug/pugsoap.cgi?wsdl
    contact:
      - FN: PubChem Help Desk
        email: [email protected]

  - name: PubChem Structure Image Service
    description: Generates 2D and 3D structure images for chemical compounds by CID, SID, SMILES, or InChI. Returns PNG images at configurable sizes, suitable for embedding in applications and documents.
    humanURL: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=PNG
    baseURL: https://pubchem.ncbi.nlm.nih.gov/rest/pug
    tags:
      - Structure Images
      - 2D Structures
      - Visualization
    properties:
      - type: Documentation
        url: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=PNG
    contact:
      - FN: PubChem Help Desk
        email: [email protected]
    operations:
      - summary: Get compound 2D structure image by CID
        method: GET
        path: /compound/cid/{cid}/PNG
        description: Returns a PNG image of the 2D chemical structure for the given compound ID. Size can be controlled with the image_size parameter.
      - summary: Get compound image by name
        method: GET
        path: /compound/name/{name}/PNG
        description: Returns a PNG image of the 2D chemical structure for a compound looked up by name.
      - summary: Get compound image by SMILES
        method: GET
        path: /compound/smiles/{smiles}/PNG
        description: Returns a PNG image of the 2D chemical structure for the compound specified by SMILES string.

  - name: PubChem Identifier Exchange Service
    description: Bulk identifier conversion service for translating between PubChem CIDs, SIDs, and external identifiers such as CAS Registry Numbers, ChEMBL IDs, ChEBI IDs, and other registry identifiers at scale.
    humanURL: https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi
    baseURL: https://pubchem.ncbi.nlm.nih.gov/idexchange
    tags:
      - Identifier Conversion
      - CAS Numbers
      - ChEMBL
      - ChEBI
      - Registry IDs
    properties:
      - type: Documentation
        url: https://pubchem.ncbi.nlm.nih.gov/docs/identifier-exchange-service
    contact:
      - FN: PubChem Help Desk
        email: [email protected]

common:
  - type: Terms of Service
    url: https://www.nlm.nih.gov/web_policies.html
  - type: Privacy Policy
    url: https://www.nlm.nih.gov/privacy.html
  - type: Status
    url: https://pubchem.ncbi.nlm.nih.gov/
  - type: Support
    url: https://support.nlm.nih.gov/
  - type: Sign Up
    url: https://www.ncbi.nlm.nih.gov/account/
  - type: GitHub
    url: https://github.com/ncbi
  - type: Blog
    url: https://pubchemblog.wordpress.com/
  - type: Documentation
    url: https://pubchem.ncbi.nlm.nih.gov/docs/
  - type: FAQ
    url: https://pubchem.ncbi.nlm.nih.gov/docs/faq
  - type: Rate Limits
    url: https://pubchem.ncbi.nlm.nih.gov/docs/programmatic-access#section=Request-Volume-Limitations
  - type: Plans
    url: plans/plans.yml
  - type: Rate Limits
    url: rate-limits/rate-limits.yml
  - type: FinOps
    url: finops/finops.yml

maintainers:
  - FN: Kin Lane
    email: [email protected]