ChEMBL Molecules Scraper

ChEMBL Molecules Scraper

Scrape ChEMBL molecules by name, ID, or type, up to a million per run. Every molecule comes with its ChEMBL ID, names, molecule type, and full metadata. No API key. Export to CSV, JSON, Excel, or XML.

ChEMBL's official API needs a web service client and returns deeply nested JSON that you must flatten yourself. This reads the public molecule endpoints directly, filters by name substring or molecule type, and returns each match in one flat row. It is the fastest way to turn ChEMBL compound data into a spreadsheet.

Who uses it	What they scrape ChEMBL for
Cheminformatics engineers	Building a local compound database for virtual screening
Drug discovery researchers	Pulling candidate molecules for a target or disease area
Data scientists	Creating training sets for molecular property prediction
Bioinformaticians	Linking molecules to bioactivity data for analysis

What it does

This Actor collects ChEMBL molecules by name substring, ChEMBL ID, or molecule type, and returns each one as a flat row.

• 🔍 Name or ID search: substring match on molecule names and synonyms, or exact ChEMBL ID.
• 🧪 Molecule type filter: Small molecule, Antibody, Enzyme, Protein, and more.
• 📄 Flat rows: one molecule per row, ready for CSV, JSON, Excel, or XML.
• ⚡ No API key: public ChEMBL endpoints, no registration or rate-limit headaches.

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

What you can do with ChEMBL data

🧪 Build a screening library.

A cheminformatics engineer pulls all small molecules matching a name substring and exports them to CSV for virtual screening.

📊 Analyze compound properties.

A data scientist collects molecules of a given type and joins them with bioactivity data to train a property prediction model.

🔗 Link molecules to targets.

A drug discovery researcher retrieves molecules by ChEMBL ID and cross-references them with target and assay data.

🗂️ Create a local ChEMBL subset.

A bioinformatician exports all molecules of a specific type to build a local database for offline analysis.

Why choose this scraper

	What you get
No API key	Public ChEMBL endpoints, no registration or OAuth
Flat output	One row per molecule, no nested JSON to parse
Flexible filters	Search by name, ID, or molecule type
Scalable	Collect up to a million molecules per run

How it compares

This Actor focuses on flat, paginated molecule metadata export, while the competitors below offer overlapping but differently packaged ChEMBL data.

Feature	ParseForge	ChEMBL Molecules Scraper - Compound Metadata	ChEMBL Drug & Molecule Scraper - Free Chemistry API	ChEMBL Bioactivity Normalizer & QC
Search by molecule name substring	Yes	Yes	Not listed	Not listed
Filter by molecule type	Yes	Yes	Not listed	Not listed
Export to CSV, JSON, Excel, XML	Yes	Not listed	Yes	Not listed
No API key required	Yes	Not listed	Yes	Not listed
Bioactivity normalization and QC	Not listed	Not listed	Not listed	Yes

Configure the run

Drive the Actor from a molecule name substring, a ChEMBL ID, or a molecule type, and set a maximum number of molecules to collect. The Input tab lists every parameter.

A first run with the defaults:

{
 "query": "aspirin",
 "maxItems": 10
}

A larger pull:

{
 "query": "aspirin",
 "maxItems": 200
}

Pricing

Pay-per-result: $0.038 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$3.80
1,000 results	$38.00
10,000 results	$380.00

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 Molecules 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-molecules-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 query. It is a substring search, so 'aspirin' works but 'aspirn' will not. Also make sure the molecule type filter is not too restrictive. Try clearing the type filter and using a shorter query.

Why is the run slow?

ChEMBL's public endpoints can be slow for large result sets. Reduce maxItems or narrow your query. The Actor uses pagination and polite delays to avoid being blocked.

Why are some fields empty?

Not all molecules have every property. For example, some may lack a molecular weight or ALogP. Empty fields are normal and reflect missing data in ChEMBL.

Can I get more than 1,000,000 molecules?

The maximum is 1,000,000 per run. If you need more, split your query into smaller chunks, for example by molecule type or name prefix, and run multiple times.

Why did I get a timeout error?

ChEMBL may be temporarily slow. Retry the run, or reduce maxItems. If the problem persists, check the ChEMBL service status.

FAQ

Question	Answer
Do I need a ChEMBL API key?	No. This Actor uses the public ChEMBL web interface, so no registration or API key is required.
Can I search by molecule name?	Yes. The query field does a substring search across molecule names and synonyms. For example, entering 'aspirin' returns acetylsalicylic acid and related entries.
Can I search by ChEMBL ID?	Yes. Enter a ChEMBL ID like CHEMBL25 in the query field to retrieve that specific molecule.
What molecule types can I filter by?	Small molecule, Antibody, Cell, Enzyme, Gene, Oligonucleotide, Oligosaccharide, Protein, and Unknown. Leave the field empty to include all types.
How many molecules can I get in one run?	You can set maxItems up to 1,000,000. The Actor will paginate through results until it reaches that number or runs out of matches.
What output formats are supported?	CSV, JSON, Excel, and XML. You can choose the format when you run the Actor or via API.
Is the data from ChEMBL free to use?	ChEMBL data is licensed under Creative Commons Attribution-Share Alike 3.0. You can use it for commercial and non-commercial purposes with attribution.
Can I schedule this Actor to run regularly?	Yes. You can set up a schedule in Apify to run it daily, weekly, or at any interval to keep your dataset up to date.
Does this Actor get bioactivity data?	No, this Actor focuses on molecule metadata. For bioactivity records, use a dedicated ChEMBL bioactivity scraper.
Can I get the SMILES string for each molecule?	Yes, the output includes the canonical SMILES for each molecule, along with other properties like molecular formula and weight.

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.