chembl-query

Research

Query ChEMBL database for bioactivity data on drug-like compounds. Use this skill when: (1) Finding compounds active against a protein target (target-based search), (2) Getting bioactivity profile for a molecule (molecule-based search), (3) Finding drugs for a disease indication (indication-based search).

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ChEMBL Query

Query ChEMBL database for bioactivity data on drug-like compounds.

When to Use

Find compounds active against a protein target (target-based search)
Get bioactivity profile for a molecule (molecule-based search)
Find drugs for a disease indication (indication-based search)

Workflow

Use Case 1: Target-Based Compound Search

Find compounds with activity against a protein target.

from open_biomed.tools.tool_registry import TOOLS

tool = TOOLS["chembl_query"]

# Search by target name
results, _ = tool.run(
    query_type="target",
    target_name="EGFR",
    standard_type="IC50",
    standard_value_lte=100,  # nM
    limit=20
)

# Or search by UniProt ID
results, _ = tool.run(
    query_type="target",
    uniprot_id="P00533",
    standard_type="IC50",
    limit=20
)

Use Case 2: Molecule Bioactivity Profile

Get all known targets and activity data for a compound.

# Search by molecule name
results, _ = tool.run(
    query_type="molecule",
    molecule_name="imatinib",
    limit=50
)

# Or search by SMILES
results, _ = tool.run(
    query_type="molecule",
    smiles="CC(=O)Oc1ccccc1C(=O)O",
    limit=20
)

# Or search by ChEMBL ID
results, _ = tool.run(
    query_type="molecule",
    chembl_id="CHEMBL25",
    limit=20
)

Use Case 3: Disease/Indication-Based Drug Search

Find drugs studied for a specific disease.

# Find all drugs for diabetes
results, _ = tool.run(
    query_type="indication",
    disease="diabetes",
    limit=50
)

# Filter for approved drugs only (max_phase=4)
results, _ = tool.run(
    query_type="indication",
    disease="diabetes",
    max_phase=4,  # Approved drugs only
    limit=20
)

Expected Outputs

Query Type	Output Fields
Target	`molecule_chembl_id`, `molecule_name`, `target_chembl_id`, `target_name`, `standard_type`, `standard_value`, `standard_units`, `pchembl_value`
Molecule	`molecule_chembl_id`, `molecule_name`, `target_chembl_id`, `target_name`, `target_organism`, `standard_type`, `standard_value`, `standard_units`, `pchembl_value`
Indication	`molecule_chembl_id`, `molecule_name`, `indication`, `max_phase_for_ind`, `phase_description`

Score Interpretation

Activity Values

pChEMBL Value	IC50/Ki Approx	Interpretation
> 9	< 1 nM	Extremely potent
8-9	1-10 nM	Very potent
7-8	10-100 nM	Potent
6-7	100 nM - 1 uM	Moderately active
5-6	1-10 uM	Weakly active
< 5	> 10 uM	Inactive

Clinical Phase

Phase	Description
0	Preclinical
1	Phase I (safety)
2	Phase II (efficacy)
3	Phase III (large-scale)
4	Approved

Parameters

Parameter	Type	Description
`query_type`	str	"target", "molecule", or "indication"
`target_name`	str	Target name (e.g., "EGFR", "BACE1")
`uniprot_id`	str	UniProt accession (e.g., "P00533")
`molecule_name`	str	Molecule name (e.g., "aspirin")
`smiles`	str	SMILES string
`chembl_id`	str	ChEMBL ID (e.g., "CHEMBL25")
`disease`	str	Disease name (e.g., "diabetes")
`standard_type`	str	Activity type (e.g., "IC50", "Ki", "EC50")
`standard_value_lte`	float	Max activity value (nM)
`max_phase`	int	Minimum clinical phase (0-4)
`limit`	int	Max results (default: 50)

Error Handling

Error	Solution
Target not found	Try alternative names or UniProt ID
No activity data	Target may not have curated bioactivity data
Molecule not found	Verify SMILES or try molecule name
No indication results	Try simpler disease terms (e.g., "neoplasm" instead of "cancer")
Timeout	Reduce limit parameter

Available Tools

Tool Name	Purpose
`chembl_query`	Unified ChEMBL query interface

See examples/basic_example.py for complete runnable examples.