🧪 PubChem Compound Scraper

🚀 Export chemistry data from PubChem in seconds. Look up 119M+ compounds by CID, name, SMILES, or InChIKey. Pull molecular formulas, weights, structures, IUPAC names, synonyms, and 23+ computed properties.

The PubChem Compound Scraper taps PubChem, the world's largest open chemistry database, maintained by the NIH National Library of Medicine. The Actor returns 19 structured fields per record, including PubChem CID, IUPAC name, molecular formula and weight, canonical and isomeric SMILES, InChI, InChIKey, computed physicochemical properties, and the full synonym list.

The catalog covers 119 million unique chemical compounds, drawn from hundreds of contributing organizations, including the FDA, EPA, DrugBank, ChEMBL, NIST, and pharma research consortia. This Actor exposes four lookup modes (CID, name, SMILES, InChIKey) and lets you cherry-pick which of 23 PubChem-computed properties to return.

🎯 Target Audience	💡 Primary Use Cases
Chemists, pharma R&D, cheminformaticians, materials scientists, drug-discovery teams, regulatory analysts, chemistry educators	Compound lookup and enrichment, SAR/QSAR feature engineering, ADMET screening inputs, regulatory dossiers, synonym normalization, structure-to-property mapping

📋 What the PubChem Compound Scraper does

Four lookup workflows in a single Actor:

• 🔢 CID lookup. Numeric PubChem identifiers like 2244 (aspirin), 3672 (ibuprofen).
• 📛 Name lookup. Common names like aspirin, caffeine, paclitaxel.
• 🧬 SMILES lookup. Pass a structure string and resolve to the canonical PubChem record.
• 🔑 InChIKey lookup. Hash-based exact-match lookup, ideal for deduplication.

Pick from 23 PubChem-computed properties (molecular formula, weight, exact mass, SMILES variants, InChI, IUPAC name, XLogP, TPSA, complexity, charge, H-bond donor/acceptor counts, rotatable bonds, heavy atoms, stereocenters, 3D volume, feature count, and more). Toggle synonym fetching to also pull every common name registered for each compound.

💡 Why it matters: PubChem is the de facto reference for compound metadata in cheminformatics. Building your own client means juggling the PUG REST API, throttling, retries, and per-property batching. This Actor delivers a tidy record per compound, ready for downstream modelling, dashboards, or reports.

📊 Data fields

Each record includes: canonicalSMILES, cid, exactMass, hBondAcceptorCount, hBondDonorCount, inchi, inchiKey, isomericSMILES, iupacName, molecularFormula, molecularWeight, properties, rotatableBondCount, scrapedAt, synonyms, title, tpsa, url, xLogP. These field names come straight from the actor's dataset schema, so what you see here is what lands in your dataset.

🚀 How to use

1. 📝 Sign up. Create a free account with $5 credit (takes 2 minutes).
2. 🌐 Open the Actor. Go to the PubChem Compound Scraper page on the Apify Store.
3. 🎯 Set input. Pick a lookup mode, paste identifiers, choose which properties to fetch.
4. 🚀 Run it. Click Start and let the Actor collect your data.
5. 📥 Download. Grab your results in the Dataset tab as CSV, Excel, JSON, or XML.

⏱️ Total time from signup to downloaded dataset: 3-5 minutes. No coding required.

🔗 Recommended Actors

• 🧬 KEGG Pathways Scraper - Biological pathways, compounds, genes, drugs
• 🏥 ClinicalTrials.gov Scraper - Global clinical research registry
• 📚 PubMed Scraper - Biomedical literature search
• 🔬 ArXiv Scraper - Preprint research papers
• 📊 GBIF Biodiversity Scraper - Global species occurrence data

💡 Pro Tip: browse the complete ParseForge collection for more reference-data scrapers.

⚠️ Disclaimer: this Actor is an independent tool and is not affiliated with, endorsed by, or sponsored by the NIH National Library of Medicine, PubChem, or any government body. All trademarks mentioned are the property of their respective owners. Only publicly available open data is collected.

🆘 Need Help?

If you hit a bug, have questions about setup, or need a scraper we haven't built yet, open our contact form or write to parseforge@protonmail.com. We also take on paid custom data projects.

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