# ChEMBL Compounds Scraper (`parseforge/chembl-compounds-scraper`) Actor

Scrapes ChEMBL compound records by clinical phase or molregno range. Returns molecule name, structure, phase, and metadata as flat rows.

- **URL**: https://apify.com/parseforge/chembl-compounds-scraper.md
- **Developed by:** [ParseForge](https://apify.com/parseforge) (community)
- **Categories:** Education, Automation, Integrations
- **Stats:** 2 total users, 1 monthly users, 89.7% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $7.50 / 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?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
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.
Actors are written with capital "A".

## 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.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

[![ParseForge](https://raw.githubusercontent.com/ParseForge/apify-assets/main/banner.jpg)](https://apify.com/parseforge?fpr=vmoqkp)

### 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:

```json
{
 "maxItems": 10
}
```

A larger pull:

```json
{
 "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](https://console.apify.com/sign-up?fpr=vmoqkp) to collect up to 1,000,000 results per run.

### Run it

1. [Create a free Apify account with $5 in credit](https://console.apify.com/sign-up?fpr=vmoqkp).
2. Open the [ChEMBL Compounds Scraper](https://apify.com/parseforge/chembl-compounds-scraper?fpr=vmoqkp).
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](https://docs.apify.com/api/v2) (`run-sync-get-dataset-items`) or the [ApifyClient](https://docs.apify.com/api/client/js) 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:

```bash
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](https://apify.com/parseforge?fpr=vmoqkp) 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.

# Actor input Schema

## `maxPhase` (type: `string`):

Filter by maximum clinical trial phase reached.

## `molRegnoMin` (type: `integer`):

Optional lower bound on the ChEMBL molregno (internal numeric ID). Use to paginate through the full catalog.

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

Maximum number of compounds to collect per run.

## Actor input object example

```json
{
  "maxItems": 10
}
```

# Actor output Schema

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

No description

# 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 = {
    "maxItems": 10
};

// Run the Actor and wait for it to finish
const run = await client.actor("parseforge/chembl-compounds-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 = { "maxItems": 10 }

# Run the Actor and wait for it to finish
run = client.actor("parseforge/chembl-compounds-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 '{
  "maxItems": 10
}' |
apify call parseforge/chembl-compounds-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,parseforge/chembl-compounds-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/8ek0nf9nQGFj9vXSj/builds/rtHaQSbNz7kkdjQK4/openapi.json