Skillintermediate

ChEMBL REST API

| Endpoint | Description | |----------|-------------| | `/molecule/{chembl_id}` | Get molecule by ChEMBL ID | | `/molecule/search?q={query}` | Free-text molecule search | | `/target/{chembl_id}` | Get target by ChEMBL ID | | `/target/search?q={query}` | Free-text target search | | `/activity?molecule_chembl_id={id}` | Activities for a molecule | | `/activity?target_chembl_id={id}` | Activities for

Claude Code Knowledge Pack7/10/2026

Overview

ChEMBL REST API

Base URL

https://www.ebi.ac.uk/chembl/api/data

Auth

No API key required. Fully open and free.

Key Endpoints

Endpoint	Description
`/molecule/{chembl_id}`	Get molecule by ChEMBL ID
`/molecule/search?q={query}`	Free-text molecule search
`/target/{chembl_id}`	Get target by ChEMBL ID
`/target/search?q={query}`	Free-text target search
`/activity?molecule_chembl_id={id}`	Activities for a molecule
`/activity?target_chembl_id={id}`	Activities for a target
`/mechanism?molecule_chembl_id={id}`	Mechanism of action
`/drug_indication?molecule_chembl_id={id}`	Drug indications
`/similarity/{smiles}/{threshold}`	Similarity search (threshold 40-100)
`/substructure/{smiles}`	Substructure search

Common Parameters

format=json — response format (default json)
limit — results per page (default 20, max 1000)
offset — pagination offset
order_by — sort field (prefix - for descending)
only — return only specified fields (comma-separated)

Filtering operators (append to field names)

__exact, __icontains, __gt, __gte, __lt, __lte, __in, __isnull, __startswith, __range, __regex

Example Calls

# Get molecule by ID
/molecule/CHEMBL25.json

# Search molecules by name
/molecule/search?q=aspirin&format=json

# Activities for a target with potency filter
/activity?target_chembl_id=CHEMBL240&pchembl_value__gte=6&format=json&limit=100

# Similarity search (80% threshold)
/similarity/CC(%3DO)Oc1ccccc1C(%3DO)O/80.json

# Approved drugs only
/molecule?max_phase=4&format=json

# Mechanism of action
/mechanism?molecule_chembl_id=CHEMBL25&format=json

Response Format (molecule)

{
  "page_meta": {"limit": 20, "offset": 0, "total_count": 150},
  "molecules": [{
    "molecule_chembl_id": "CHEMBL25",
    "pref_name": "ASPIRIN",
    "max_phase": 4,
    "molecule_properties": {
      "full_mwt": 180.16, "full_molformula": "C9H8O4",
      "alogp": 1.31, "hba": 3, "hbd": 1, "psa": 63.60
    },
    "molecule_structures": {
      "canonical_smiles": "CC(=O)Oc1ccccc1C(=O)O",
      "standard_inchi_key": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
    }
  }]
}

Rate Limits

No strict limit. Keep under ~10 req/sec. No auth required.