PubChem Compound Scraper

Look up chemical compounds by name in PubChem — the world's largest free chemistry database with 100+ million compounds. Returns CID, molecular formula, weight, SMILES, InChI, IUPAC name, physicochemical properties, description and synonyms.

Features

• Resolves common names, synonyms, and IUPAC names to PubChem CID
• Batch mode: comma-separated list of compound names in a single run
• Configurable output fields — only fetch what you need
• Returns canonical SMILES, InChI, InChIKey, XLogP, H-bond donors/acceptors
• Optional narrative description (up to 600 chars from PubChem/MeSH)
• Optional top-10 synonyms list
• Rate-limited at 5 req/sec (PubChem public limit)

Input

Field	Type	Required	Default	Description
compoundName	string	✅	—	Compound name(s), comma-separated for batch
outputFields	array		["formula","weight","smiles","description"]	Fields to include

Available output fields: formula, weight, smiles, iupac, xlogp, hbond_donor, hbond_acceptor, rotatable_bonds, inchi, inchikey, complexity, description, synonyms

Output

{
  "compoundName": "aspirin",
  "cid": 2244,
  "formula": "C9H8O4",
  "molecularWeight": 180.16,
  "smiles": "CC(=O)Oc1ccccc1C(=O)O",
  "iupacName": "2-acetyloxybenzoic acid",
  "inchi": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
  "inchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "xlogp": 1.2,
  "hbondDonors": 1,
  "hbondAcceptors": 4,
  "description": "Aspirin is a member of the class of benzoic acids that is salicylic acid in which the hydrogen of the phenolic hydroxy group has been replaced by an acetyl group.",
  "url": "https://pubchem.ncbi.nlm.nih.gov/compound/2244"
}

Use Cases

1. Drug Database Enrichment

A pharmaceutical data team inputs a list of 200 active pharmaceutical ingredients and retrieves full physicochemical profiles (formula, MW, XLogP, SMILES, InChI) in a single run — enriching their compound database for ADME modeling.

2. Chemistry Education Platform

An online chemistry platform uses this actor to power compound lookup widgets — students enter a drug name and instantly see the molecular formula, 3D-ready SMILES string and IUPAC name pulled live from PubChem.

3. Cheminformatics Pipeline

A bioinformatics researcher building a machine learning model for drug solubility batch-looks up 500 compound names to get their SMILES strings, XLogP values and H-bond counts — feeding directly into RDKit for descriptor calculation.

Data Source

PubChem PUG REST API — NCBI/NIH, no API key required.

Pricing

Pay-per-result on Apify. 100 compounds ≈ $0.50–$1.00.