# ChEMBL Scraper - Compounds, Drugs & Properties (`logiover/chembl-compound-scraper`) Actor

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.

- **URL**: https://apify.com/logiover/chembl-compound-scraper.md
- **Developed by:** [Logiover](https://apify.com/logiover) (community)
- **Categories:** Developer tools
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $3.50 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

Learn more: https://docs.apify.com/actors/running/actors-in-store.md#pay-per-event

## What's an Apify Actor?

An Actor is a serverless cloud program that runs on the Apify platform. It has two run modes.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.

Apify vocabulary and the platform model are defined once, in the agent quickstart at https://apify.com/agents.md.

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.

Do not guess an integration path. Every one of them is in the agent quickstart at https://apify.com/agents.md: the Apify MCP server, Agent Skills with the Apify CLI, the JavaScript and Python clients, the REST API, and the account-free path for an agent with no human to sign in. It also carries the rule on stating cost before the first paid run.

For examples already wired to this Actor's own input schema, see the [API](#api) section below.

Each client library has reference documentation the quickstart does not restate: [JavaScript/TypeScript](https://docs.apify.com/api/client/js/docs.md) (`npm install apify-client`) and [Python](https://docs.apify.com/api/client/python/docs.md) (`pip install apify-client`).

# README

## ChEMBL Scraper - Compounds, Drugs & Properties

![Apify Actor](https://img.shields.io/badge/Apify-Actor-00A67E?logo=apify\&logoColor=white) ![No API key](https://img.shields.io/badge/No%20API%20key-required-2ea44f) ![Pay per result](https://img.shields.io/badge/Pricing-Pay%20per%20result-1C7ED6) ![Export](https://img.shields.io/badge/Export-JSON%20%7C%20CSV%20%7C%20Excel-F59E0B)

**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.**

***

### 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

```json
{
  "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

```json
{
  "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

```json
{
  "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**

```bash
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**

```javascript
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**

```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](https://apify.com/logiover/uniprot-protein-scraper) — Protein targets and sequences
- [PubChem Scraper](https://apify.com/logiover/pubchem-scraper) — Chemical substance data
- [ClinicalTrials.gov Scraper](https://apify.com/logiover/clinicaltrials-gov-scraper) — Trials for the same compounds
- [FDA Data Scraper](https://apify.com/logiover/fda-data-scraper) — Approvals and safety data

# Actor input Schema

## `searchTerms` (type: `array`):

Compound names to match, e.g. aspirin, statin. Leave empty to export every compound that matches the phase filter below.

## `minPhase` (type: `string`):

Restrict to compounds that reached at least this phase. 4 means approved drugs only.

## `maxPagesPerSearch` (type: `integer`):

How many result pages to walk for each search. Set 0 for no limit.

## `maxItems` (type: `integer`):

Stop after this many compounds. Set 0 for no limit.

## `maxConcurrency` (type: `integer`):

Parallel requests. Lower this if the source rate-limits you.

## `proxyConfiguration` (type: `object`):

Proxy used to fetch pages. Defaults to Apify Proxy (automatic). You usually do not need to change this.

## Actor input object example

```json
{
  "searchTerms": [],
  "minPhase": "4",
  "maxPagesPerSearch": 4,
  "maxItems": 500,
  "maxConcurrency": 2,
  "proxyConfiguration": {
    "useApifyProxy": true
  }
}
```

# Actor output Schema

## `results` (type: `string`):

All compounds extracted in this run.

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "searchTerms": [],
    "maxPagesPerSearch": 4,
    "maxItems": 500,
    "maxConcurrency": 2
};

// Run the Actor and wait for it to finish
const run = await client.actor("logiover/chembl-compound-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "searchTerms": [],
    "maxPagesPerSearch": 4,
    "maxItems": 500,
    "maxConcurrency": 2,
}

# Run the Actor and wait for it to finish
run = client.actor("logiover/chembl-compound-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "searchTerms": [],
  "maxPagesPerSearch": 4,
  "maxItems": 500,
  "maxConcurrency": 2
}' |
apify call logiover/chembl-compound-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,logiover/chembl-compound-scraper"
        }
    }
}
```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/zFMtc7Piz7Dscl44K/builds/65CYrbsU7An40N7vL/openapi.json