PubChem Compound Scraper

Scrape PubChem — the world's largest free chemistry database with 100M+ compounds maintained by the NCBI. Search by compound name, PubChem CID, SMILES string, or free-text query. Returns molecular identifiers, physicochemical properties, structural data, and synonyms. HTTP-only via the public PubChem REST API. No auth, no proxy required.

What this actor does

• Four modes: searchByName, searchBySmiles, searchByCid, fullTextSearch
• Compound lookup: by IUPAC name, common name, CID, or SMILES notation
• Rich properties: molecular formula, weight, SMILES, InChI, InChIKey, XLogP, H-bond counts, heavy atom count, complexity
• Synonyms: up to 10 synonyms per compound
• Empty fields are omitted — no nulls in output

Output per compound

Field	Type	Description
cid	integer	PubChem Compound ID
iupacName	string	IUPAC systematic name
molecularFormula	string	Molecular formula (e.g. C9H8O4)
molecularWeight	float	Molecular weight in g/mol
canonicalSmiles	string	Canonical SMILES notation
isomericSmiles	string	Isomeric SMILES (with stereochemistry)
inchiKey	string	Standard InChIKey hash
inchi	string	Standard InChI string
xlogp	float	Computed XLogP3 lipophilicity
exactMolecularWeight	float	Exact monoisotopic mass
hbondDonorCount	integer	Number of hydrogen bond donors
hbondAcceptorCount	integer	Number of hydrogen bond acceptors
heavyAtomCount	integer	Number of heavy (non-hydrogen) atoms
rotatablebondCount	integer	Number of rotatable bonds
synonyms	array	Up to 10 common synonyms
sourceUrl	string	PubChem compound page URL
recordType	string	Always "compound"
scrapedAt	string	ISO 8601 timestamp

Input

Field	Type	Default	Description
mode	string	searchByName	searchByName / searchBySmiles / searchByCid / fullTextSearch
compoundNames	array	[]	Compound names to look up (mode=searchByName)
smilesList	array	[]	SMILES strings (mode=searchBySmiles)
cids	array	[]	PubChem CIDs (mode=searchByCid)
searchQuery	string	aspirin	Free-text query (mode=fullTextSearch)
maxItems	integer	10	Max compounds to return (1–1000)

Example: look up common drug compounds

{
  "mode": "searchByName",
  "compoundNames": ["aspirin", "caffeine", "ibuprofen", "acetaminophen"],
  "maxItems": 4
}

Example: search by SMILES

{
  "mode": "searchBySmiles",
  "smilesList": ["CC(=O)Oc1ccccc1C(=O)O", "Cn1cnc2c1c(=O)n(c(=O)n2C)C"],
  "maxItems": 2
}

Example: full-text search

{
  "mode": "fullTextSearch",
  "searchQuery": "acetylsalicylic acid",
  "maxItems": 5
}

FAQs

Do I need an API key? No. PubChem's REST API is freely accessible with no authentication required.

Are there rate limits? PubChem allows up to 5 requests per second. This actor enforces a 0.2s delay between requests automatically.

How many compounds can I scrape? Up to 1000 per run. For fullTextSearch, the actor fetches matching CIDs first, then retrieves full data for each.

What is the difference between canonical and isomeric SMILES? Canonical SMILES is a standardized representation without stereochemistry. Isomeric SMILES includes stereochemical information (E/Z, R/S).

Can I search by molecular structure? Yes, use searchBySmiles mode with a valid SMILES string.

Why are some fields missing from certain compounds? Not all compounds in PubChem have complete property sets. The actor omits any field for which PubChem returns no data.

What is XLogP? XLogP3 is a computed measure of lipophilicity (fat-solubility) — key for predicting drug absorption, distribution, and bioavailability.