ChEMBL Compounds Scraper

ChEMBL Compounds Scraper

Scrape ChEMBL compound records by clinical phase or internal ID, up to a million per run. Each row returns the molecule name, structure, phase, and metadata. No API key or registration. Export to CSV, JSON, Excel, or XML.

The ChEMBL database holds millions of manually curated bioactive molecules, but the official API requires learning a complex query language and paginating through large result sets. This Actor reads the public compound catalog directly, letting you filter by maximum clinical trial phase or paginate by internal molregno. You get a flat, analysis-ready dataset without writing a single line of code.

Who uses it	What they scrape ChEMBL for
Cheminformatics researchers	Building a local dataset of drug-like molecules for virtual screening.
Pharma business analysts	Tracking which compounds have reached Phase 3 or approval in a therapeutic area.
Bioinformatics students	Gathering a labeled set of molecules for a machine learning project.
Drug repurposing teams	Extracting all approved small molecules to cross-reference with new targets.

What it does

This Actor collects ChEMBL compound records filtered by clinical phase or molregno range and returns each molecule as a flat row.

• 💊 Clinical phase filter: restrict results to Preclinical, Phase 1, 2, 3, or Approved compounds only.
• 🔢 Molregno pagination: set a starting molregno to resume a previous scrape or walk the entire catalog in chunks.
• 📦 Bulk export: collect up to one million compounds per run and download as CSV, JSON, Excel, or XML.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with ChEMBL data

🧪 Build a virtual screening library.

A cheminformatician scrapes all Phase 2 and Phase 3 compounds to create a focused docking library for a new protein target.

📈 Monitor the clinical pipeline.

A pharma analyst runs the Actor weekly with the Approved phase filter to track newly approved small molecules across all therapeutic areas.

🎓 Teach drug discovery with real data.

A university lecturer exports a set of preclinical compounds with SMILES strings for a hands-on molecular modelling practical.

🔄 Cross-reference drug repurposing candidates.

A research team scrapes all approved molecules and joins them against internal assay results to flag potential repurposing opportunities.

Why choose this scraper

	What you get
No API key	Reads the public ChEMBL data feeds directly, no registration or token management.
Flat schema	Every compound returns as one row with consistent columns, ready for pandas or Excel.
Phase targeting	Pull only molecules that reached a specific clinical trial stage.
Resumable runs	Use the molregno range to paginate through the entire ChEMBL catalog across multiple runs.

How it compares

This Actor focuses on high-volume compound catalog extraction with phase filtering and molregno pagination, while the competitors below offer different ChEMBL scraping approaches.

Feature	ParseForge	ChEMBL Drug & Molecule Scraper	ChEMBL Molecules Scraper
Clinical phase filter	Yes, filter by Preclinical through Approved	Not listed	Not listed
Molregno pagination	Yes, set a lower bound to resume or chunk runs	Not listed	Not listed
Up to 1M compounds per run	Yes	Not listed	Not listed
SMILES and InChI output	Yes	Yes	Yes
Molecular weight and ALogP	Yes	Yes	Yes

Configure the run

Drive the Actor with an optional maximum clinical phase and an optional starting molregno. Filters run as each compound is read so only matching records reach your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
 "maxItems": 10
}

A larger pull:

{
 "maxItems": 200
}

Pricing

Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$0.85
1,000 results	$8.50
10,000 results	$85.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the ChEMBL Compounds Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to ChEMBL through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/chembl-compounds-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check your Max Phase filter. If you set it to a low phase like Preclinical, and the molregno range you specified contains only later-phase compounds, no records will match. Try widening the filter or removing the molregno lower bound.

The run stopped before reaching my Maximum compounds limit.

The Actor stops when it exhausts the available records matching your filters. If you are paginating with Mol Regno Min, increase the starting value and run again to continue from where you left off.

Some compounds are missing SMILES or InChI strings.

Not all ChEMBL records have complete structural data. Missing values are expected for some older or less characterized entries and will appear as empty cells in your dataset.

The run is taking a long time.

Large requests with a high Maximum compounds value and no phase filter will scan many records. Use the phase filter to narrow the scope, or reduce the maximum items for faster test runs.

FAQ

Question	Answer
Do I need a ChEMBL API key?	No. The Actor reads the public ChEMBL data feeds directly, so no registration or API key is required.
What data fields does each compound row include?	Each row includes the ChEMBL ID, molecule name, molecular formula, molecular weight, ALogP, SMILES, InChI, clinical phase, and other metadata. The exact fields are shown in the sample output on the Actor's page.
How do I scrape the entire ChEMBL database?	Set a high Maximum compounds limit and leave the filters empty. For more than one million records, run the Actor multiple times using the Mol Regno Min field to paginate through the catalog.
Can I filter by molecular weight or other properties?	The Actor filters by clinical phase and molregno range during collection. For property-based filtering, export the full dataset and filter in your analysis tool.
What is a molregno?	The molregno is ChEMBL's internal numeric identifier for each molecule. You can use it to paginate through the database or resume a previous scrape from a specific point.
How do I get only approved drugs?	Set the Max Phase filter to 'Approved (Phase 4)'. The Actor will return only compounds that have reached the approved phase.
What export formats are supported?	You can export your dataset as CSV, JSON, Excel, or XML from the Apify platform.
Is this Actor suitable for large-scale cheminformatics projects?	Yes. The Actor can collect up to one million compounds per run, and you can chain multiple runs using the molregno pagination to build a complete local copy of ChEMBL.
Does this Actor include bioactivity data?	This Actor focuses on compound metadata. For bioactivity records, consider a dedicated ChEMBL bioactivity scraper.
How often is the ChEMBL data updated?	The Actor reads the live ChEMBL data feeds, so each run reflects the latest public release from EMBL-EBI.

Related actors

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by EMBL-EBI. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.