substructure_search

MCP tool from PubChem MCP Server by Augmented-Nature

Find compounds containing substructures

How to use it

substructure_search is exposed by the PubChem MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the substructure_search tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.

FULL PUBCHEM MCP SERVER LISTING

Other tools in PubChem MCP Server (29)

analyze_molecular_complexity

Synthetic accessibility

analyze_stereochemistry

Chirality and isomer analysis

assess_drug_likeness

Lipinski Rule of Five analysis

assess_environmental_fate

Biodegradation analysis

batch_compound_lookup

Bulk processing (up to 200 compounds)

calculate_descriptors

Comprehensive molecular descriptors

compare_activity_profiles

Cross-compound comparisons

get_3d_conformers

3D structural information

Detailed assay protocols

get_compound_bioactivities

All activity data for compounds

get_compound_info

Detailed compound information by CID

get_compound_properties

Molecular weight, logP, TPSA, etc.

get_compound_synonyms

All names and synonyms

get_external_references

Links to ChEMBL, DrugBank, etc.

get_literature_references

PubMed citations

get_pharmacophore_features

Pharmacophore mapping

get_regulatory_info

FDA, EPA regulations

get_safety_data

GHS hazard classifications

get_toxicity_info

LD50, carcinogenicity data

predict_admet_properties

ADMET predictions

search_bioassays

Find biological assays

search_by_cas_number

CAS Registry Number lookup

search_by_inchi

InChI/InChI key search

search_by_smiles

Exact SMILES string matching

search_by_target

Find compounds tested against targets

search_compounds

Search by name, CAS number, formula, or identifier

Chemical patent information

search_similar_compounds

Tanimoto similarity search

superstructure_search

Find larger compounds containing query