ChEMBL Scraper - Compounds, Drugs & Properties

Scrape the ChEMBL bioactivity database in bulk. Extract ChEMBL ID, preferred name, SMILES, InChI key, molecular formula and weight, ALogP, Lipinski violations, development phase, ATC codes and trade names to CSV/JSON. No API key.

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What does the ChEMBL Scraper do?

This Actor turns ChEMBL data into a structured dataset. You point it at every approved drug or by compound name, it walks the result pages one after another, and it writes one clean row per compound into your dataset — ready to export as JSON, CSV or Excel, or to pull straight from the Apify API.

ChEMBL is the EBI's curated database of bioactive molecules and exposes a keyless REST API with plain offset paging. The Actor reads that API directly, flattening the nested property and structure objects into one row per compound so that SMILES, molecular properties and development phase all arrive as ordinary columns. Pagination is followed automatically until it runs out of results, hits your page limit or hits your Max items cap, whichever comes first. Every row is de-duplicated across the whole run, so you are never billed twice for the same compound.

There is no API key, no login and no browser involved. That keeps runs fast and cheap, and it means you can schedule the Actor without worrying about credentials expiring.

Who is it for?

• Medicinal chemists assembling compound sets for a target class.
• Cheminformatics teams building descriptor tables and training sets.
• Drug-discovery analysts tracking what reached each clinical phase.
• AI teams collecting SMILES corpora for generative chemistry.
• Academic researchers exporting compound metadata for a review.

Use cases

• Export approved drugs with their ATC codes and trade names.
• Pull SMILES strings in bulk for a machine-learning pipeline.
• Filter compounds by Lipinski rule-of-five violations for drug-likeness.
• Compare molecular properties across a series of related compounds.
• Find withdrawn or black-box-warning drugs for safety analysis.

Why use this ChEMBL Scraper?

• 🔑 Keyless — no account, no API token, no cookies to paste.
• 📦 32 fields per compound — everything the source exposes, already typed.
• 📄 Real pagination — it walks page after page instead of returning the first screen.
• 🎯 Precise caps — Max items stops the run exactly where you want it, so the bill is predictable.
• 📊 Export anywhere — JSON, CSV, Excel or HTML, plus the Apify API and integrations.
• 💸 Pay per result — you pay for rows you actually receive, with no platform fees to calculate.

What data can you extract?

Every run produces one row per compound, with these fields:

Field	Type	Description
chemblId	string	ChEMBL compound identifier
prefName	string	Preferred compound name
moleculeType	string	Molecule type, e.g. Small molecule or Protein
maxPhase	number	Highest development phase reached, 4 means approved
firstApproval	number	Year of first approval when applicable
atcCodes	string	WHO ATC classification codes, separated by a pipe
synonyms	string	Known synonyms, separated by a pipe
tradeNames	string	Registered trade names, separated by a pipe
canonicalSmiles	string	Canonical SMILES structure string
standardInchiKey	string	Standard InChI key
molecularFormula	string	Full molecular formula
molecularWeight	number	Full molecular weight
alogp	number	Calculated ALogP lipophilicity
psa	number	Polar surface area
hba	number	Hydrogen bond acceptors
hbd	number	Hydrogen bond donors
aromaticRings	number	Number of aromatic rings
heavyAtoms	number	Number of heavy atoms
rotatableBonds	number	Number of rotatable bonds
ro5Violations	number	Lipinski rule-of-five violations
qedWeighted	number	Weighted QED drug-likeness score
isOral	boolean	Administered orally
isParenteral	boolean	Administered parenterally
isTopical	boolean	Administered topically
blackBoxWarning	boolean	Carries a black-box safety warning
withdrawnFlag	boolean	Withdrawn from at least one market
naturalProduct	boolean	Derived from a natural product
prodrug	boolean	Acts as a prodrug
compoundUrl	string	ChEMBL report card URL
query	string	Search term this row came from
page	number	Result page the compound appeared on
scrapedAt	string	ISO timestamp of extraction

Output example

{
  "alogp": 1.31,
  "aromaticRings": 1,
  "atcCodes": "B01AC06 | N02BA01 | N02BA51 | A01AD05 | N02BA71",
  "blackBoxWarning": false,
  "canonicalSmiles": "CC(=O)Oc1ccccc1C(=O)O",
  "chemblId": "CHEMBL25",
  "compoundUrl": "https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL25/",
  "firstApproval": 1950,
  "hba": 3,
  "hbd": 1,
  "heavyAtoms": 13,
  "isOral": true,
  "isParenteral": false,
  "isTopical": false,
  "maxPhase": 4,
  "molecularFormula": "C9H8O4",
  "molecularWeight": 180.16,
  "moleculeType": "Small molecule",
  "naturalProduct": false,
  "page": 1,
  "prefName": "ASPIRIN",
  "prodrug": false,
  "psa": 63.6,
  "qedWeighted": 0.55,
  "query": "aspirin",
  "ro5Violations": 0,
  "rotatableBonds": 2,
  "scrapedAt": "2026-09-18T09:16:02.771Z",
  "standardInchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "synonyms": "Acetylsalicylic acid | Aspirin | Bayer | Ecotrin",
  "tradeNames": "8-HOUR BAYER | ECOTRIN",
  "withdrawnFlag": false
}

How to use

Option A — every approved drug

{
  "maxItems": 2000,
  "maxPagesPerSearch": 10,
  "minPhase": "4",
  "searchTerms": []
}

1. Open the Actor and fill in the first field.
2. Set the page limit and Max items to bound the run.
3. Click Start, then export from the Output tab.

Option B — by compound name

{
  "maxItems": 1000,
  "maxPagesPerSearch": 4,
  "minPhase": "any",
  "searchTerms": [
    "aspirin",
    "statin"
  ]
}

Everything in the first field is processed independently, so you can batch several targets into one run and split them apart afterwards.

Input parameters

Parameter	Type	Default	Description
searchTerms	array	–	Compound names to match, e.
minPhase	string	4	Restrict to compounds that reached at least this phase.
maxPagesPerSearch	integer	4	How many result pages to walk for each search.
maxItems	integer	500	Stop after this many compounds.
maxConcurrency	integer	2	Parallel requests.
proxyConfiguration	object	{"useApifyProxy": true}	Proxy used to fetch pages.

Tips for best results

• Leave the search term empty to walk the whole database — roughly 2.9 million compounds.
• A search term matches the preferred name, so aspirin or statin both work.
• Minimum development phase 4 restricts the run to approved drugs.
• The API returns up to 1,000 compounds per request, so exports need few calls.
• canonicalSmiles is the column to feed into RDKit or any cheminformatics toolkit.
• ro5Violations of 0 or 1 is the usual drug-likeness filter.
• Flags such as isOral are published as 0 or 1 in ChEMBL; the Actor converts them to real booleans, so 0 stays false rather than becoming empty.
• Most research compounds have no prefName, atcCodes or firstApproval — that is a gap in the source, not extraction.
• Keep concurrency low — the EBI runs this API free for the whole community.
• Pair with the UniProt scraper to connect compounds back to their protein targets.

Integrations

Send results straight into the tools you already use: Google Sheets, Slack, Zapier, Make, Airtable or any Webhook. You can also schedule the Actor to run hourly, daily or weekly and have each run append to the same dataset, which is how you build a price or availability history rather than a one-off snapshot.

API usage

Run the Actor and collect results from any language. Replace <YOUR_TOKEN> with your Apify API token.

cURL

curl -X POST "https://api.apify.com/v2/acts/logiover~chembl-compound-scraper/run-sync-get-dataset-items?token=<YOUR_TOKEN>" \
  -H "Content-Type: application/json" \
  -d '{"maxItems": 2000, "maxPagesPerSearch": 10, "minPhase": "4", "searchTerms": []}'

Node.js

import { ApifyClient } from 'apify-client';

const client = new ApifyClient({ token: '<YOUR_TOKEN>' });
const run = await client.actor('logiover/chembl-compound-scraper').call({"maxItems": 2000, "maxPagesPerSearch": 10, "minPhase": "4", "searchTerms": []});
const { items } = await client.dataset(run.defaultDatasetId).listItems();
console.log(items);

Python

from apify_client import ApifyClient

client = ApifyClient('<YOUR_TOKEN>')
run = client.actor('logiover/chembl-compound-scraper').call(run_input={"maxItems": 2000, "maxPagesPerSearch": 10, "minPhase": "4", "searchTerms": []})
for item in client.dataset(run['defaultDatasetId']).iterate_items():
    print(item)

Use with AI agents (MCP)

This Actor is available through the Apify MCP server, so an AI agent can call it as a tool. Point your agent at https://mcp.apify.com and it can run the ChEMBL Scraper on demand — for example: "Pull the first 500 compounds from ChEMBL and summarise what you find." The agent receives the same structured rows you would get from the UI.

FAQ

Do I need a ChEMBL account or API key?

No. The Actor reads publicly available data only. There is nothing to authenticate and no credentials to rotate.

How many compounds can I get in one run?

As many as the source exposes. Raise the page limit and Max items together; the run stops at whichever limit it reaches first.

Why did I get fewer rows than I asked for?

The source ran out of compounds. That is normal for narrow searches — broaden the query or add more targets to one run.

Are results de-duplicated?

Yes. Each compound is emitted once per run, even when it appears on several pages, so you are never billed twice for the same record.

Why are some fields empty?

ChEMBL does not publish every attribute for every compound. Empty means the source did not supply it, not that extraction failed.

What export formats are supported?

JSON, CSV, Excel, HTML and RSS from the Output tab, plus the Apify API and any integration you connect.

How fast is it?

It is pure HTTP with no browser, so a page of results typically takes a second or two. Raise Max concurrency carefully — the source rate-limits aggressive crawling.

Can I schedule it?

Yes. Use the Apify scheduler to run it on any interval and append each run to the same dataset for time-series analysis.

Does it work behind a proxy?

It uses Apify Proxy automatically. You can switch groups or supply your own proxies in Proxy configuration.

How often does the data change?

ChEMBL updates continuously. Re-run whenever you need current data; the Actor always reads the live source, never a cache.

Is the output schema stable?

Yes. Field names and types are fixed, so downstream pipelines will not break between runs.

What if the source changes its format?

Open an issue on the Issues tab and it gets fixed. The Actor is actively maintained.

Is it legal?

This Actor reads only publicly available data from ChEMBL — the same content any visitor or client sees without logging in. It does not bypass authentication, does not collect private data and does not attempt to defeat access controls. You are responsible for how you use the output: respect the source's terms of service, applicable copyright, and data-protection law such as GDPR where personal data is involved. Scraping public data is generally lawful in the EU and the US, but the responsibility for the downstream use of that data sits with you.

Related scrapers

• UniProt Scraper — Protein targets and sequences
• PubChem Scraper — Chemical substance data
• ClinicalTrials.gov Scraper — Trials for the same compounds
• FDA Data Scraper — Approvals and safety data