PubChem Chemical Compound Scraper

Scrape PubChem — the world's largest free chemistry database with 100M+ compounds maintained by the NCBI. Search by compound name or PubChem CID, fetch detailed molecular properties, or retrieve all known synonyms. HTTP-only via the public PubChem REST API. No API key, no proxy required.

What this actor does

• Four modes: searchCompounds, getByName, getByCID, getSynonyms
• Name-based search: returns multiple matching compounds for a query term
• Exact lookup: get full detail for a specific compound name or CID
• Synonyms: retrieve all known names and identifiers for any compound
• Rich properties: molecular formula, weight, SMILES, InChI, InChIKey, XLogP, H-bond counts, heavy atom count, complexity, charge
• Empty fields are omitted — no nulls in output

Modes

Mode	Description
searchCompounds	Search by keyword — returns multiple matching compounds
getByName	Get detailed info for an exact compound name
getByCID	Get compound by PubChem CID number
getSynonyms	Get all known synonyms for a compound

Input

Field	Type	Description
mode	select	Which mode to use (default: searchCompounds)
compoundName	string	Compound name to search or look up (e.g. aspirin, caffeine)
cid	integer	PubChem CID for getByCID or getSynonyms mode
maxItems	integer	Maximum records to return, 1–200 (default: 20)

Output per compound

Field	Type	Description
cid	integer	PubChem Compound ID
iupacName	string	IUPAC systematic name
commonName	string	Common/trade name (first synonym or provided name)
molecularFormula	string	Molecular formula (e.g. C9H8O4)
molecularWeight	float	Molecular weight in g/mol
canonicalSmiles	string	Canonical SMILES notation
inchiKey	string	Standard InChIKey hash
xLogP	float	Computed XLogP3 lipophilicity
hBondDonorCount	integer	Number of hydrogen bond donors
hBondAcceptorCount	integer	Number of hydrogen bond acceptors
rotatableBondCount	integer	Number of rotatable bonds
heavyAtomCount	integer	Number of heavy (non-hydrogen) atoms
complexity	float	Molecular complexity score
charge	integer	Formal charge of the compound
synonyms	array	Top 5 known synonyms
pubchemUrl	string	Direct link to PubChem compound page
scrapedAt	string	ISO 8601 timestamp of when the record was scraped

Data source

PubChem is a free chemistry database maintained by the National Center for Biotechnology Information (NCBI), part of the US National Institutes of Health. The PubChem REST API is completely free with no registration required — rate limited to 5 requests/second.

Example output

{
  "cid": 2244,
  "iupacName": "2-(acetyloxy)benzoic acid",
  "commonName": "aspirin",
  "molecularFormula": "C9H8O4",
  "molecularWeight": 180.16,
  "canonicalSmiles": "CC(=O)Oc1ccccc1C(=O)O",
  "inchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "xLogP": 1.2,
  "hBondDonorCount": 1,
  "hBondAcceptorCount": 4,
  "rotatableBondCount": 3,
  "heavyAtomCount": 13,
  "complexity": 212,
  "charge": 0,
  "synonyms": ["aspirin", "acetylsalicylic acid", "2-acetoxybenzoic acid", "ASA", "Ecotrin"],
  "pubchemUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/2244",
  "scrapedAt": "2026-06-03T10:00:00+00:00"
}

FAQs

Do I need an API key? No. The PubChem REST API is completely free and requires no registration.

How many results can I get? Up to 200 compounds per run. The PubChem database contains over 100 million compounds.

What is the rate limit? PubChem allows up to 5 requests per second. This actor respects that limit automatically.

Can I look up by SMILES or InChI? Use getByName mode — PubChem's name endpoint also accepts SMILES strings and InChI identifiers.

What if a compound has no IUPAC name? Fields are only included when data is available. If an IUPAC name is missing, only the commonName (from synonyms) will appear.

Is the data current? PubChem is updated continuously by the NCBI. Data accuracy reflects the current PubChem database state.