---
title: PubChem search
description: 'Look up PubChem by CID, name or structure, pull properties, run Tanimoto similarity and substructure queries, and export CSV or SDF inside PUG REST limits.'
tags:
  - pubchem
---

PubChem lets you search chemistry by structure, similarity, or computed property across the world's largest free compound repository — canonical SMILES, InChI, molecular weight, LogP, TPSA, and more. Reach for it when you want broad structure-based lookup or property enrichment rather than target-specific bioactivity. When you already know the target and want measured activity data, use its sibling [ChEMBL](/docs/chembl) instead. See [what you can achieve](/docs/capabilities#chemistry).

## PubChem integration in .bloom* platform

PubChem is NCBI's comprehensive open repository of chemical substances and compounds, aggregating data from over 1,000 contributing data sources. It is the world's largest free chemistry database. .bloom* integrates PubChem two ways: ask Ivy in chat and it runs PubChem lookups inside that turn, or open the **PubChem Database Search** form in the Tools panel to submit a tracked PubChem job.

## Citations & Resources

> Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2023 update. *Nucleic Acids Research*. 2023 Jan 6;51(D1):D1373-D1380. doi: [10.1093/nar/gkac956](https://doi.org/10.1093/nar/gkac956)

> **Website**: [https://pubchem.ncbi.nlm.nih.gov](https://pubchem.ncbi.nlm.nih.gov)

> **PUG REST API**: [https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest](https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest)

## Webapp search and retrieval capabilities

### Search methods in .bloom*

**Compound identifier lookup:**
- **CID search**: Direct PubChem Compound ID (e.g., 2244 for aspirin)
- **Name search**: Chemical names, synonyms, and common identifiers
- **SMILES/InChI search**: Structure-based searching with automatic format detection
- **CAS number lookup**: Registry identifier searches

**Batch processing:**
- **In chat**: paste or upload a list of names, SMILES or CIDs; a lookup covers 10 at a time, so Ivy runs larger lists in batches
- **In the form**: the Batch Processing operation takes a comma-separated list of CIDs

### Data retrieval and enrichment

**Chemical identifiers:**
- **Canonical SMILES**: Standardized structure representation
- **Isomeric SMILES**: Stereochemistry-preserving SMILES
- **InChI and InChIKey**: IUPAC International Chemical Identifier
- **Synonyms**: Multiple chemical names and identifiers
- **CAS numbers**: Chemical Abstracts Service registry numbers

**Physicochemical properties:**
- **Molecular weight**: Exact molecular mass calculations
- **Molecular formula**: Elemental composition
- **LogP**: Partition coefficient estimates (multiple methods)
- **TPSA**: Topological polar surface area
- **Hydrogen bond donors/acceptors**: HBD/HBA counts
- **Rotatable bonds**: Molecular flexibility assessment

**Structural information:**
- **2D coordinates**: Structure visualization and editing
- **3D conformers**: Multiple conformational representations
- **Substructure information**: Functional group annotations
- **Bioassay links**: Connection to biological activity data

## Integration with .bloom* workflows

### Compound database enrichment

**Vendor search preparation:**
- Standardize compound identifiers before supplier searches
- Add canonical SMILES for consistent structure handling
- Include physicochemical properties for filtering and analysis

**Hit list enhancement:**
- Add calculated properties to screening results
- Cross-reference structures with known compounds
- Validate compound identities from external sources

**Library characterization:**
- Analyze physicochemical property distributions
- Identify compound classes and structural patterns
- Generate property-based filtering criteria

### Research applications

**Drug discovery support:**
- Access to millions of known chemical structures
- Property-based compound selection and filtering
- Integration with virtual screening workflows

**Chemical informatics:**
- Large-scale property calculations
- Structure-property relationship studies
- Compound library diversity analysis

**Regulatory compliance:**
- Access to standardized identifiers
- Reference data for safety assessments
- Cross-validation of chemical information

## Webapp interface features

### The PubChem Database Search form

The form in the Tools panel offers five operations, each submitted as a PubChem job you can track in your job history:

- **Compound Identification**: convert compound names to CIDs
- **Comprehensive Search**: complete compound data, optionally with molecular properties
- **Fragment Library Generation**: fragment-like compounds, optionally filtered by the Rule of 3 (MW ≤ 300, HBD ≤ 3, HBA ≤ 3)
- **Similarity Analysis**: structurally similar compounds above a threshold
- **Batch Processing**: a comma-separated list of CIDs

### In chat

Ask Ivy for a compound lookup, property lookup, similarity search or substructure search; see [search](/docs/pubchem/search) for what each takes and returns. Ivy can filter the results by property ranges and save them as CSV or SDF in the chat's [code workspace](/docs/sandbox).

## Data quality and limitations

### Coverage considerations

**Data completeness:**
- Not all compounds have complete property sets
- Some older entries lack modern calculated properties
- Bioassay data availability varies by compound

**Data currency:**
- PubChem is continuously updated
- .bloom* caches results to optimize performance
- Fresh data retrieval available on demand

### Technical limitations

**Rate limiting (PUG REST API):**
- No more than **5 requests per second**
- No more than **400 requests per minute**
- No longer than **300 seconds running time per minute**
- .bloom* implements intelligent caching and queuing to respect these limits

**Data scope:**
- Focus on small molecules and natural products
- Limited coverage of large biomolecules
- No commercial pricing or availability information

## Workflow integration patterns

### Compound sourcing pipeline

1. **Initial search**: Use PubChem to identify compounds of interest
2. **Property enrichment**: Add physicochemical and structural data
3. **Vendor cross-check**: Validate against commercial suppliers
4. **Procurement planning**: Generate purchase lists with standardized identifiers

### Virtual screening preparation

1. **Library curation**: Select compounds from PubChem collections
2. **Property filtering**: Apply drug-like criteria and ADMET filters
3. **Format standardization**: Convert to consistent SMILES/InChI formats
4. **Docking preparation**: Feed to DiffDock or other modeling tools

### Research data management

1. **Data standardization**: Normalize identifiers across datasets
2. **Metadata enrichment**: Add calculated properties and annotations
3. **Quality control**: Validate compound structures and data
4. **Analysis preparation**: Format data for statistical and cheminformatics tools

## Chat Usage

### Example Prompts

- "Fetch aspirin from PubChem"
- "Search PubChem for EGFR inhibitors and their properties"
- "Run a similarity search for compounds like gefitinib at 70% Tanimoto similarity"
- "Find compounds in PubChem containing a benzimidazole substructure"

### Workflow Chaining

- **Feeds into**: ADMET-AI/ADMETLab3 (screening), DiffDock (docking), Compound Passport, AiZynthFinder (synthesis)
- **Accepts from**: Free-text compound names, SMILES strings from other tools

### Search tools

| Ask Ivy to ... | What runs |
|----------------|-----------|
| Look up compounds by name, SMILES or CID (up to 10 at once) | PubChem compound lookup |
| Get the full property set for one compound | PubChem property lookup |
| Find analogs above a Tanimoto threshold | PubChem similarity search |
| Find compounds containing a given substructure | PubChem substructure search |

## FAQ

### What data does PubChem provide?

  Structures, synonyms, identifiers, properties, and assay links curated by NCBI.

### Can I do structure search?

  Yes. Give Ivy a SMILES, InChIKey, CID or name for exact or similarity matches, or a SMILES or SMARTS pattern for substructure matches.

### How do I export?

  Ask Ivy to save the results as CSV or SDF with the identifiers and properties you need. See [exports](/docs/pubchem/export).

## Read next