# PubChem Chemical Compound Scraper (`crawlerbros/pubchem-chemical-compound-scraper`) Actor

Search PubChem - the world's largest free chemistry database with 100M+ compounds. Search by name, get by CID, or fetch synonyms. Returns molecular formula, weight, SMILES, InChI, logP, H-bond counts, and more. No API key required.

- **URL**: https://apify.com/crawlerbros/pubchem-chemical-compound-scraper.md
- **Developed by:** [Crawler Bros](https://apify.com/crawlerbros) (community)
- **Categories:** Developer tools, Automation, Integrations
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, NaN bookmarks
- **User rating**: No ratings yet

## Pricing

from $3.00 / 1,000 results

This Actor is paid per event and usage. You are charged both the fixed price for specific events and for Apify platform usage.
Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have.

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

## What's an Apify Actor?

Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases.
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.

In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js.md):

```bash
npm install apify-client
```

In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.md):

```bash
pip install apify-client
```

In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md):

````bash
# MacOS / Linux
curl -fsSL https://apify.com/install-cli.sh | bash
# Windows
irm https://apify.com/install-cli.ps1 | iex
```bash

In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp.md).

If your project is in a different language, use 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

## PubChem Chemical Compound Scraper

Scrape **PubChem** — the world's largest free chemistry database with 100M+ compounds maintained by the NCBI. Search by compound name or PubChem CID, fetch detailed molecular properties, or retrieve all known synonyms. HTTP-only via the public PubChem REST API. No API key, no proxy required.

### What this actor does

- **Four modes:** `searchCompounds`, `getByName`, `getByCID`, `getSynonyms`
- **Name-based search:** returns multiple matching compounds for a query term
- **Exact lookup:** get full detail for a specific compound name or CID
- **Synonyms:** retrieve all known names and identifiers for any compound
- **Rich properties:** molecular formula, weight, SMILES, InChI, InChIKey, XLogP, H-bond counts, heavy atom count, complexity, charge
- **Empty fields are omitted** — no nulls in output

### Modes

| Mode | Description |
|---|---|
| `searchCompounds` | Search by keyword — returns multiple matching compounds |
| `getByName` | Get detailed info for an exact compound name |
| `getByCID` | Get compound by PubChem CID number |
| `getSynonyms` | Get all known synonyms for a compound |

### Input

| Field | Type | Description |
|---|---|---|
| `mode` | select | Which mode to use (default: `searchCompounds`) |
| `compoundName` | string | Compound name to search or look up (e.g. aspirin, caffeine) |
| `cid` | integer | PubChem CID for `getByCID` or `getSynonyms` mode |
| `maxItems` | integer | Maximum records to return, 1–200 (default: 20) |

### Output per compound

| Field | Type | Description |
|---|---|---|
| `cid` | integer | PubChem Compound ID |
| `iupacName` | string | IUPAC systematic name |
| `commonName` | string | Common/trade name (first synonym or provided name) |
| `molecularFormula` | string | Molecular formula (e.g. C9H8O4) |
| `molecularWeight` | float | Molecular weight in g/mol |
| `canonicalSmiles` | string | Canonical SMILES notation |
| `inchiKey` | string | Standard InChIKey hash |
| `xLogP` | float | Computed XLogP3 lipophilicity |
| `hBondDonorCount` | integer | Number of hydrogen bond donors |
| `hBondAcceptorCount` | integer | Number of hydrogen bond acceptors |
| `rotatableBondCount` | integer | Number of rotatable bonds |
| `heavyAtomCount` | integer | Number of heavy (non-hydrogen) atoms |
| `complexity` | float | Molecular complexity score |
| `charge` | integer | Formal charge of the compound |
| `synonyms` | array | Top 5 known synonyms |
| `pubchemUrl` | string | Direct link to PubChem compound page |
| `scrapedAt` | string | ISO 8601 timestamp of when the record was scraped |

### Data source

[PubChem](https://pubchem.ncbi.nlm.nih.gov/) is a free chemistry database maintained by the National Center for Biotechnology Information (NCBI), part of the US National Institutes of Health. The PubChem REST API is completely free with no registration required — rate limited to 5 requests/second.

### Example output

```json
{
  "cid": 2244,
  "iupacName": "2-(acetyloxy)benzoic acid",
  "commonName": "aspirin",
  "molecularFormula": "C9H8O4",
  "molecularWeight": 180.16,
  "canonicalSmiles": "CC(=O)Oc1ccccc1C(=O)O",
  "inchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "xLogP": 1.2,
  "hBondDonorCount": 1,
  "hBondAcceptorCount": 4,
  "rotatableBondCount": 3,
  "heavyAtomCount": 13,
  "complexity": 212,
  "charge": 0,
  "synonyms": ["aspirin", "acetylsalicylic acid", "2-acetoxybenzoic acid", "ASA", "Ecotrin"],
  "pubchemUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/2244",
  "scrapedAt": "2026-06-03T10:00:00+00:00"
}
````

### FAQs

**Do I need an API key?**
No. The PubChem REST API is completely free and requires no registration.

**How many results can I get?**
Up to 200 compounds per run. The PubChem database contains over 100 million compounds.

**What is the rate limit?**
PubChem allows up to 5 requests per second. This actor respects that limit automatically.

**Can I look up by SMILES or InChI?**
Use `getByName` mode — PubChem's name endpoint also accepts SMILES strings and InChI identifiers.

**What if a compound has no IUPAC name?**
Fields are only included when data is available. If an IUPAC name is missing, only the `commonName` (from synonyms) will appear.

**Is the data current?**
PubChem is updated continuously by the NCBI. Data accuracy reflects the current PubChem database state.

# Actor input Schema

## `mode` (type: `string`):

How to search for compounds. searchCompounds returns multiple matches for a name; getByName returns detailed info for an exact name; getByCID looks up a compound by PubChem CID; getSynonyms returns all synonyms for a compound.

## `compoundName` (type: `string`):

Name of the compound to search for or look up (e.g. aspirin, caffeine, ethanol). Used in searchCompounds, getByName, and getSynonyms modes.

## `cid` (type: `integer`):

PubChem Compound ID for getByCID mode (e.g. 2244 for aspirin, 2519 for caffeine).

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

Maximum number of compounds to return (1–200). Default is 20.

## Actor input object example

```json
{
  "mode": "searchCompounds",
  "compoundName": "aspirin",
  "maxItems": 20
}
```

# Actor output Schema

## `compounds` (type: `string`):

Dataset containing all scraped PubChem compound records with molecular properties and identifiers.

# 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 = {
    "mode": "searchCompounds",
    "compoundName": "aspirin",
    "maxItems": 20
};

// Run the Actor and wait for it to finish
const run = await client.actor("crawlerbros/pubchem-chemical-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 = {
    "mode": "searchCompounds",
    "compoundName": "aspirin",
    "maxItems": 20,
}

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

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

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

```

## CLI example

```bash
echo '{
  "mode": "searchCompounds",
  "compoundName": "aspirin",
  "maxItems": 20
}' |
apify call crawlerbros/pubchem-chemical-compound-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "command": "npx",
            "args": [
                "mcp-remote",
                "https://mcp.apify.com/?tools=crawlerbros/pubchem-chemical-compound-scraper",
                "--header",
                "Authorization: Bearer <YOUR_API_TOKEN>"
            ]
        }
    }
}

```

## OpenAPI specification

```json
{
    "openapi": "3.0.1",
    "info": {
        "title": "PubChem Chemical Compound Scraper",
        "description": "Search PubChem - the world's largest free chemistry database with 100M+ compounds. Search by name, get by CID, or fetch synonyms. Returns molecular formula, weight, SMILES, InChI, logP, H-bond counts, and more. No API key required.",
        "version": "1.0",
        "x-build-id": "hCG15WHDgEPQmYZN8"
    },
    "servers": [
        {
            "url": "https://api.apify.com/v2"
        }
    ],
    "paths": {
        "/acts/crawlerbros~pubchem-chemical-compound-scraper/run-sync-get-dataset-items": {
            "post": {
                "operationId": "run-sync-get-dataset-items-crawlerbros-pubchem-chemical-compound-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK"
                    }
                }
            }
        },
        "/acts/crawlerbros~pubchem-chemical-compound-scraper/runs": {
            "post": {
                "operationId": "runs-sync-crawlerbros-pubchem-chemical-compound-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor and returns information about the initiated run in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK",
                        "content": {
                            "application/json": {
                                "schema": {
                                    "$ref": "#/components/schemas/runsResponseSchema"
                                }
                            }
                        }
                    }
                }
            }
        },
        "/acts/crawlerbros~pubchem-chemical-compound-scraper/run-sync": {
            "post": {
                "operationId": "run-sync-crawlerbros-pubchem-chemical-compound-scraper",
                "x-openai-isConsequential": false,
                "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.",
                "tags": [
                    "Run Actor"
                ],
                "requestBody": {
                    "required": true,
                    "content": {
                        "application/json": {
                            "schema": {
                                "$ref": "#/components/schemas/inputSchema"
                            }
                        }
                    }
                },
                "parameters": [
                    {
                        "name": "token",
                        "in": "query",
                        "required": true,
                        "schema": {
                            "type": "string"
                        },
                        "description": "Enter your Apify token here"
                    }
                ],
                "responses": {
                    "200": {
                        "description": "OK"
                    }
                }
            }
        }
    },
    "components": {
        "schemas": {
            "inputSchema": {
                "type": "object",
                "required": [
                    "mode"
                ],
                "properties": {
                    "mode": {
                        "title": "Mode",
                        "enum": [
                            "searchCompounds",
                            "getByName",
                            "getByCID",
                            "getSynonyms"
                        ],
                        "type": "string",
                        "description": "How to search for compounds. searchCompounds returns multiple matches for a name; getByName returns detailed info for an exact name; getByCID looks up a compound by PubChem CID; getSynonyms returns all synonyms for a compound.",
                        "default": "searchCompounds"
                    },
                    "compoundName": {
                        "title": "Compound name",
                        "type": "string",
                        "description": "Name of the compound to search for or look up (e.g. aspirin, caffeine, ethanol). Used in searchCompounds, getByName, and getSynonyms modes."
                    },
                    "cid": {
                        "title": "PubChem CID",
                        "minimum": 1,
                        "type": "integer",
                        "description": "PubChem Compound ID for getByCID mode (e.g. 2244 for aspirin, 2519 for caffeine)."
                    },
                    "maxItems": {
                        "title": "Max items",
                        "minimum": 1,
                        "maximum": 200,
                        "type": "integer",
                        "description": "Maximum number of compounds to return (1–200). Default is 20.",
                        "default": 20
                    }
                }
            },
            "runsResponseSchema": {
                "type": "object",
                "properties": {
                    "data": {
                        "type": "object",
                        "properties": {
                            "id": {
                                "type": "string"
                            },
                            "actId": {
                                "type": "string"
                            },
                            "userId": {
                                "type": "string"
                            },
                            "startedAt": {
                                "type": "string",
                                "format": "date-time",
                                "example": "2025-01-08T00:00:00.000Z"
                            },
                            "finishedAt": {
                                "type": "string",
                                "format": "date-time",
                                "example": "2025-01-08T00:00:00.000Z"
                            },
                            "status": {
                                "type": "string",
                                "example": "READY"
                            },
                            "meta": {
                                "type": "object",
                                "properties": {
                                    "origin": {
                                        "type": "string",
                                        "example": "API"
                                    },
                                    "userAgent": {
                                        "type": "string"
                                    }
                                }
                            },
                            "stats": {
                                "type": "object",
                                "properties": {
                                    "inputBodyLen": {
                                        "type": "integer",
                                        "example": 2000
                                    },
                                    "rebootCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "restartCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "resurrectCount": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "computeUnits": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            },
                            "options": {
                                "type": "object",
                                "properties": {
                                    "build": {
                                        "type": "string",
                                        "example": "latest"
                                    },
                                    "timeoutSecs": {
                                        "type": "integer",
                                        "example": 300
                                    },
                                    "memoryMbytes": {
                                        "type": "integer",
                                        "example": 1024
                                    },
                                    "diskMbytes": {
                                        "type": "integer",
                                        "example": 2048
                                    }
                                }
                            },
                            "buildId": {
                                "type": "string"
                            },
                            "defaultKeyValueStoreId": {
                                "type": "string"
                            },
                            "defaultDatasetId": {
                                "type": "string"
                            },
                            "defaultRequestQueueId": {
                                "type": "string"
                            },
                            "buildNumber": {
                                "type": "string",
                                "example": "1.0.0"
                            },
                            "containerUrl": {
                                "type": "string"
                            },
                            "usage": {
                                "type": "object",
                                "properties": {
                                    "ACTOR_COMPUTE_UNITS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_WRITES": {
                                        "type": "integer",
                                        "example": 1
                                    },
                                    "KEY_VALUE_STORE_LISTS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_INTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_EXTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_RESIDENTIAL_TRANSFER_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_SERPS": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            },
                            "usageTotalUsd": {
                                "type": "number",
                                "example": 0.00005
                            },
                            "usageUsd": {
                                "type": "object",
                                "properties": {
                                    "ACTOR_COMPUTE_UNITS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATASET_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "KEY_VALUE_STORE_WRITES": {
                                        "type": "number",
                                        "example": 0.00005
                                    },
                                    "KEY_VALUE_STORE_LISTS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_READS": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "REQUEST_QUEUE_WRITES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_INTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "DATA_TRANSFER_EXTERNAL_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_RESIDENTIAL_TRANSFER_GBYTES": {
                                        "type": "integer",
                                        "example": 0
                                    },
                                    "PROXY_SERPS": {
                                        "type": "integer",
                                        "example": 0
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
    }
}
```