chembl-query
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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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- QSong-github/DrugClaw★ 116same name
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The file
Files
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.
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