Title99/100
Search Compounds
The title clearly communicates the tool’s action and subject. Keep it concise.
Description97/100
Search for chemical compounds in ChEMBL database by name, ChEMBL ID, or molecular structure. WHEN TO USE compound_search vs drug_search: • compound_search: Use for ANY molecule lookup by name, ID, or structure (may lack clinical data) • drug_search: Use ONLY when searching by therapeutic indication (e.g., "drugs for diabetes") For a simple drug name lookup like "find aspirin", use compound_search. SEARCH STRATEGIES: • By name: Use 'name' for drug names, synonyms, or trade names (case-insensitive, partial match) • By ID: Use 'chembl_id' for direct lookup when you know the exact identifier (e.g., 'CHEMBL25' for aspirin) • By structure: Use 'smiles' with 'similarity_threshold' (70-100%) for finding structurally similar compounds • Substructure: Use 'smiles' without threshold to find compounds containing that substructure SIMILARITY SEARCH (uses Morgan fingerprints, radius 2, 2048 bits via FPSim2): • 70%: Loose similarity (finds diverse analogs) • 80%: Good starting threshold (finds close analogs) • 90%+: Very strict (finds nearly identical compounds) MAX_PHASE VALUES (clinical development stage): • 4 = Approved (marketed drug, e.g., FDA/EMA approved) • 3 = Phase 3 Clinical Trials • 2 = Phase 2 Clinical Trials (includes INN applications) • 1 = Phase 1 Clinical Trials (includes USAN applications) • 0.5 = Early Phase 1 • -1 = Unknown clinical phase • NULL = Preclinical compound (bioactivity data only) RETURNED DATA INCLUDES: • Molecular properties: MW, ALogP (lipophilicity), PSA, HBA, HBD, rotatable bonds, aromatic rings • QED (Quantitative Estimate of Drug-likeness): 0-1 scale, higher = more drug-like • Chirality: 0=racemic, 1=single stereoisomer, 2=achiral, -1=unchecked • Rule of Five: MW<500, ALogP<5, HBD<5, HBA<10 (compounds with 0-1 violations are Ro5 compliant) • ATC classifications, cross-references to external databases, molecule hierarchy (parent/salt forms) TIPS: • For approved drugs, add max_phase=4 • ChEMBL uses compound 'families' - salts map to parent compounds • Use get_bioactivity after finding compounds to get their target activities • Properties are calculated on parent (salt-free) form EXAMPLES: • Find aspirin: name='aspirin' or chembl_id='CHEMBL25' • Find kinase inhibitors: name='nib', max_phase=4 • Find structural analogs: Use SMILES with similarity_threshold=80
The description explains the capability, when to use it, and what to expect.
Inputs75/100
Remove validation rules already expressed in this field’s schema; describe its meaning and usage instead.
name
Compound name or synonym to search for (e.g., 'aspirin', 'imatinib'). Case-insensitive search. This is the primary search criterion.
Clear enough to supply this argument.
chembl_id
ChEMBL identifier (e.g., 'CHEMBL25' for aspirin)
Remove validation rules already expressed in this field’s schema; describe its meaning and usage instead.
smiles
SMILES structure for similarity search. Requires similarity_threshold parameter
Clarify units, where to obtain this value, or conventions not already expressed in the schema.
similarity_threshold
Similarity threshold percentage for structure search (70-100). Only used with SMILES search
Remove validation rules already expressed in this field’s schema; describe its meaning and usage instead.
max_phase
Filter by clinical phase. Use 4 for approved drugs only
Remove validation rules already expressed in this field’s schema; describe its meaning and usage instead.
limit
Maximum number of results to return
Remove validation rules already expressed in this field’s schema; describe its meaning and usage instead.
Annotations100/100
All four behavior hints are declared.
{
"title": "Search Compounds",
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}Output schema79/100
The output schema explains the structured result.
View output schema
{
"type": "object",
"required": [
"count",
"total",
"compounds"
],
"properties": {
"count": {
"type": "integer",
"description": "Number of compounds returned in this response"
},
"total": {
"type": "integer",
"description": "Total number of matching compounds available"
},
"compounds": {
"type": "array",
"items": {
"type": "object",
"required": [
"molecule_chembl_id"
],
"properties": {
"oral": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the drug is orally available"
},
"inchi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "InChI representation"
},
"score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Search relevance score"
},
"orphan": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Orphan drug designation"
},
"smiles": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "SMILES representation"
},
"prodrug": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Pro-drug indicator"
},
"topical": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the drug can be administered topically"
},
"synonyms": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"default": null,
"description": "List of synonyms and trade names"
},
"chirality": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Chirality (0=racemic, 1=single stereoisomer, 2=achiral)"
},
"inchi_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "InChI key"
},
"max_phase": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Maximum clinical trial phase (0=Preclinical, 4=Approved)"
},
"pref_name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Preferred name"
},
"usan_stem": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "USAN stem"
},
"usan_year": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "USAN application year"
},
"parenteral": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the drug can be administered parenterally"
},
"veterinary": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Veterinary product indicator"
},
"polymer_flag": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Small molecule polymer indicator"
},
"usan_substem": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "USAN substem"
},
"helm_notation": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "HELM standard notation for peptides/oligonucleotides"
},
"molecule_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Type of molecule (e.g., Small molecule)"
},
"chemical_probe": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Chemical probe indicator"
},
"first_approval": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Year of first approval"
},
"first_in_class": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "First compound of its class"
},
"inorganic_flag": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Inorganic molecule indicator"
},
"structure_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Structure type (MOL/SEQ/NONE)"
},
"withdrawn_flag": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the drug has been withdrawn"
},
"natural_product": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the molecule is a natural product"
},
"cross_references": {
"anyOf": [
{
"type": "array",
"items": {
"type": "object",
"properties": {
"xref_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "External reference ID"
},
"xref_src": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "External database source"
},
"xref_name": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "External reference name"
}
},
"description": "External database cross-reference."
}
},
{
"type": "null"
}
],
"default": null,
"description": "External database references"
},
"dosed_ingredient": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Dosed in this form"
},
"therapeutic_flag": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the molecule is therapeutic"
},
"availability_type": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Availability type (0=discontinued, 1=prescription, 2=OTC)"
},
"black_box_warning": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether the drug has a black box warning"
},
"molecule_chembl_id": {
"type": "string",
"description": "ChEMBL identifier for the molecule"
},
"molecule_hierarchy": {
"anyOf": [
{
"type": "object",
"properties": {
"active_chembl_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Active form ChEMBL ID"
},
"parent_chembl_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Parent molecule ChEMBL ID"
},
"molecule_chembl_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "This molecule's ChEMBL ID"
}
},
"description": "Parent/active molecule relationship hierarchy."
},
{
"type": "null"
}
],
"default": null,
"description": "Parent/active molecule IDs"
},
"atc_classifications": {
"anyOf": [
{
"type": "array",
"items": {
"type": "object",
"properties": {
"level1": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 1 code"
},
"level2": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 2 code"
},
"level3": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 3 code"
},
"level4": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 4 code"
},
"level5": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 5 code (full code)"
},
"level1_description": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 1 description"
},
"level2_description": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 2 description"
},
"level3_description": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 3 description"
},
"level4_description": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "ATC level 4 description"
}
},
"description": "ATC (Anatomical Therapeutic Chemical) classification."
}
},
{
"type": "null"
}
],
"default": null,
"description": "ATC classification codes"
},
"molecule_properties": {
"anyOf": [
{
"type": "object",
"properties": {
"hba": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of hydrogen bond acceptors"
},
"hbd": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of hydrogen bond donors"
},
"psa": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Polar surface area"
},
"rtb": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of rotatable bonds"
},
"alogp": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Calculated ALogP (lipophilicity)"
},
"full_mwt": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Full molecular weight"
},
"ro3_pass": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Rule of three pass (Y/N)"
},
"heavy_atoms": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of heavy atoms"
},
"mw_freebase": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Molecular weight of parent compound"
},
"qed_weighted": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Quantitative estimate of drug-likeness"
},
"aromatic_rings": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of aromatic rings"
},
"med_chem_friendly": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Med-chem friendliness indicator (Y/N)"
},
"molecular_formula": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Molecular formula"
},
"molecular_species": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Molecular species type (ACID, BASE, NEUTRAL, ZWITTERION)"
},
"np_likeness_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Natural product likeness score"
},
"num_ro5_violations": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of Lipinski rule of five violations"
}
},
"description": "Molecular properties of a compound."
},
{
"type": "null"
}
],
"default": null,
"description": "Molecular properties"
},
"usan_stem_definition": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "USAN stem definition"
}
},
"description": "Represents a chemical compound from ChEMBL."
},
"description": "List of matching compounds"
}
},
"description": "Response from compound search."
}