⚗️ ChEMBL Compounds Scraper

🚀 Export ChEMBL chemical compounds in seconds. ChEMBL IDs, names, molecular formulas, weights, SMILES, InChI, and clinical phases — direct from the public ChEMBL REST API.

🕒 Last updated. 2026-06-05 · 📊 12 fields per record · more than two million bioactive molecules curated by ChEMBL at EBI · Public API · No login required

The ChEMBL Compounds Scraper turns the ChEMBL REST API public endpoint into a clean, structured dataset. It queries the source live, normalizes the response into one row per record, and pushes the result into an Apify dataset you can download or pipe to your warehouse.

More than two million bioactive molecules curated by ChEMBL at EBI are covered in a single run, with stable field names and null-safe parsing.

🎯 Target Audience	💡 Primary Use Cases
💊 Medicinal chemists	Inventory bioactive compound space
🧪 Drug discovery	Filter by clinical phase for repurposing
🎓 Educators	Build cheminformatics teaching sets
🤖 ML teams	Train molecular property predictors

📋 What the ChEMBL Compounds Scraper does

• Calls the public ChEMBL REST API endpoint with the parameters you supply.
• Parses the response and flattens each record into a single dataset row.
• Casts numeric fields to numbers where applicable for clean spreadsheet imports.
• Surfaces rate-limit or upstream errors as a single-row error record instead of crashing.
• Exports to every Apify dataset format supported in the UI.

💡 Why it matters. The raw ChEMBL REST API response is great for API consumers but awkward for spreadsheets and BI tools. This actor normalizes the shape so the data drops straight into pandas, BigQuery, or a Google Sheet.

🎬 Full Demo

🚧 Coming soon.

⚙️ Input

Field	Type	Required	Description
maxPhase	string	No	Filter by maximum clinical trial phase reached.
molRegnoMin	integer	No	Optional lower bound on the ChEMBL molregno (internal numeric ID). Use to paginate through the full catalog.
maxItems	integer	No	Free users. 10. Paid users. up to 1,000,000. Prefill. 10.

Example 1.

{
  "maxPhase": "-1",
  "molRegnoMin": 1,
  "maxItems": 10
}

Example 2.

{
  "maxPhase": "-1",
  "molRegnoMin": 1,
  "maxItems": 50
}

⚠️ Good to Know. This actor calls the public ChEMBL REST API endpoint with no authentication required. Upstream rate limits apply; if the source returns a limit notice, you will see it as a single error record in your dataset.

📊 Output

Each record is a flat object. error is always last.

Field	Type	Description
🔹 chembl_id	string	Field from the ChEMBL REST API response.
🔹 pref_name	string	Field from the ChEMBL REST API response.
🔹 molecular_formula	string	Field from the ChEMBL REST API response.
🔹 mw	string	Field from the ChEMBL REST API response.
🔹 canonical_smiles	string	Field from the ChEMBL REST API response.
🔹 inchi	string	Field from the ChEMBL REST API response.
🔹 max_phase	string	Field from the ChEMBL REST API response.
🔹 indication_class	string	Field from the ChEMBL REST API response.
🔹 atc_classifications	string	Field from the ChEMBL REST API response.
🔹 structure_type	string	Field from the ChEMBL REST API response.
🔹 scrapedAt	string	Field from the ChEMBL REST API response.
🔹 error	string	Set if the upstream response was an error or rate-limit.

Sample record.

{
  "chembl_id": "sample_chembl_id",
  "pref_name": "sample_pref_name",
  "molecular_formula": "sample_molecular_formula",
  "mw": "sample_mw",
  "canonical_smiles": "sample_canonical_smiles",
  "inchi": "sample_inchi",
  "max_phase": "sample_max_phase",
  "indication_class": "sample_indication_class",
  "atc_classifications": "sample_atc_classifications",
  "structure_type": "sample_structure_type",
  "scrapedAt": "sample_scrapedAt",
  "error": null
}

✨ Why choose this Actor

| 🆓 | Works with the public ChEMBL REST API endpoint. No API key, no signup. | | 🧹 | Clean field names, ready for BI tools. | | 🔢 | Numeric strings cast to real numbers where it makes sense. | | 🛟 | Upstream errors and rate limits surface as a clean error record. | | 🔌 | One-click export to every Apify dataset format. | | 💾 | Push to dataset, then pipe to BigQuery, Snowflake, Postgres, or Google Sheets. |

📈 How it compares to alternatives

Approach	Setup time	Clean shape	Pagination	Error handling
Roll your own fetch	30 min +	❌	manual	manual
Copy-paste from the browser	5 min, fragile	❌	❌	❌
This Actor	5 sec, no install	✅	✅	✅

🚀 How to use

1. Click Try for free.
2. Fill in the input (or leave defaults).
3. Click Start.
4. Within seconds, the dataset is ready for download or integration.

💼 Business use cases

📊 Analytics. Pipe records into your warehouse and join against internal data for cross-source dashboards.

🤖 Automation. Trigger this actor on a schedule, then push results to Slack, Airtable, or Google Sheets.

🧪 Research. Snapshot the public state of ChEMBL REST API on a date and archive it for reproducible studies.

📰 Editorial. Verify quotes, numbers, or records cited in stories with a one-click fresh pull.

🔌 Automating ChEMBL Compounds Scraper

• Make / Zapier. Trigger this actor on a schedule, push results to Slack, Airtable, Google Sheets, or anywhere else.
• Cron schedule. Use the native Apify scheduler to run on any cadence.
• Webhooks. Get a POST to your endpoint the moment a run finishes.
• Pipe to BigQuery / Snowflake / Postgres. Native Apify integrations move datasets straight into your warehouse.

🌟 Beyond business use cases

🎓 Education. Build classroom datasets without paying for a commercial feed.

🧪 Personal research. Track changes in the source over time on your own schedule.

🤝 Non-profit and open data. Build public dashboards without writing client code.

🧰 Tinkering and prototyping. Wire up a fresh data feed in seconds to test a new chart or model.

🤖 Ask an AI assistant about this scraper

Pop this README into ChatGPT, Claude, or any AI assistant and ask it to map your specific workflow to the actor's inputs. The schema, examples, and field list above contain everything an LLM needs to design a working pipeline.

❓ Frequently Asked Questions

❓ Do I need an API key? No. This actor calls the public ChEMBL REST API endpoint with no authentication required.

❓ Is there a rate limit? The upstream source may rate-limit aggressive use. If you hit a limit, the actor pushes a single error record rather than crashing.

❓ Which formats can I download? Every format Apify's dataset UI supports.

❓ Are values cast to numbers? Where the source returns numeric strings for numeric fields, yes.

❓ How do you handle upstream errors? A single record with a populated error field is pushed, then the actor exits cleanly.

❓ Can I schedule runs? Yes. Use Apify's native scheduler, Make, Zapier, or cron.

❓ Is this scraping or API? API. The ChEMBL REST API endpoint is fully public; this actor only normalizes the response.

❓ Will the schema change? Core fields are stable. Optional fields surface as null when the source omits them.

❓ How fresh is the data? Each run hits the live endpoint, so the data is as fresh as the source allows.

❓ Can I filter the output? Yes. The input fields above let you narrow the result set before it lands in your dataset.

🔌 Integrate with any app

Apify ships native integrations with Make, Zapier, Slack, Discord, Google Drive, Google Sheets, Gmail, Airbyte, Keboola, Telegram, GitHub, and any REST API or webhook endpoint. Trigger runs from a calendar event, a form submission, a cron job, or pipe results straight into BigQuery, Snowflake, or a Postgres warehouse.

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