---
title: ZINC Quickstart
description: 'Run a first ZINC lookup by asking Ivy in chat: search by SMILES or ZINC ID, have Ivy filter by molecular weight and logP, then export the SMILES with their ZINC IDs.'
---

## Quick ZINC compound search with .bloom* platform

The ZINC database is a free resource of commercially available compounds for virtual screening, developed by the Irwin and Shoichet Laboratories at UCSF. **ZINC-22**, the latest major version, contains over **37 billion enumerated compounds** in 2D and **750+ million purchasable compounds** with 3D representations.

## Citations

> Tingle BI, Tang KG, Castanon M, Gutierrez JJ, Khurelbaatar M, Dandarchuluun C, Moroz YS, Irwin JJ. ZINC-22—A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. *Journal of Chemical Information and Modeling*. 2023;63(4):1166-1176. doi: [10.1021/acs.jcim.2c01253](https://doi.org/10.1021/acs.jcim.2c01253)

> **Website**: [https://zinc.docking.org](https://zinc.docking.org)

## Database highlights

- Hundreds of millions of purchasable compounds in ready-to-dock 3D formats
- **37+ billion compounds** searchable in 2D (make-on-demand libraries)
- Includes catalogs from **Enamine REAL**, **WuXi GalaXi**, and **Mcule Ultimate**
- Free access via CartBlanche22 interface, Globus, AWS, and Oracle OCI clouds

## Step-by-step compound library creation

There is no ZINC form or search page in .bloom*. You run a ZINC lookup by asking Ivy in chat, and it runs inside that turn — no job to track.

### 1. Ask in chat

```
Find purchasable ZINC compounds that exactly match CC(=O)Oc1ccccc1C(=O)O
Find close ZINC analogs of gefitinib and list their vendor codes
Look up ZINC000000000001 and check vendor availability
Which ZINC compounds match catalog code EN300-19380?
```

### 2. What the lookup can do

- **Search by SMILES**: an exact match, or close analogs by graph edit distance (1-4 is the useful range; wider distances return looser matches). Up to 1,000 results, 100 by default.
- **Look up ZINC IDs**: up to 100 at once, returning SMILES, vendor codes and catalog names.
- **Check vendor catalog codes**: up to 100 at once, returning the matching ZINC IDs and SMILES.
- **Fields returned**: ZINC ID, SMILES, tranche, molecular weight and logP by default; ask for reactivity, purchasability or features if you need them.

The lookup does not filter by property range, run a Tanimoto similarity search, or match a SMARTS pattern. Ivy does those steps in the chat's [code workspace](/docs/sandbox) with RDKit, on the compounds the lookup returned or on a bulk pull from ZINC's CartBlanche22 service (see [Property Filters](/docs/zinc/filters) and [Downloads & Batching](/docs/zinc/downloads)).

### 3. Review and export

- Results come back in the chat turn as a compound list with ZINC IDs, SMILES and vendor codes
- Ask Ivy to save the list as a CSV, or to convert it to 3D SDF for docking ([3D Prep & SDF Exports](/docs/zinc/3d))
- Ask Ivy to send the compounds on to another tool, such as DiffDock or ADMET-AI

## Common ZINC search scenarios

Each scenario below combines a ZINC lookup with property and structural-alert filtering that Ivy applies in the code workspace. Describe the scenario in chat and Ivy runs both parts.

### Drug-like compound library
1. Set MW: 150-500 Da, logP: -2 to 5, TPSA: <140
2. Choose "in-stock" subset for immediate availability
3. Enable PAINS and reactivity filters
4. Export 1000-5000 compounds for virtual screening

### Fragment-based screening
1. Set MW: 100-300 Da for fragment-sized molecules
2. Adjust logP and solubility properties
3. Use substructure search for specific scaffolds
4. Focus on high-quality, well-characterized fragments

### Natural product-like diversity
1. Use higher MW ranges (300-600 Da)
2. Include more complex ring systems
3. Apply natural product-inspired filters
4. Sample diverse chemical space for novelty

### ADMET-optimized compounds
1. Set properties favorable for drug development
2. Filter for good solubility and permeability
3. Exclude compounds with known liabilities
4. Generate focused libraries for hit-to-lead

## Quality control and validation

### Search result validation

**Compound quality:**
- [ ] Check SMILES validity (use structure preview)
- [ ] Verify molecular properties match expectations
- [ ] Review for unusual or reactive functional groups
- [ ] Confirm compounds are in appropriate subset

**Data completeness:**
- [ ] Ensure all requested properties are present
- [ ] Check for missing values in critical fields
- [ ] Validate ZINC IDs for uniqueness
- [ ] Review timestamp for data freshness

### Search optimization

**Performance considerations:**
- Start with smaller result sets for query testing
- Use property filters early to reduce search scope
- Consider search complexity vs. result quality trade-off
- Save successful search parameters for reuse

**Result quality assessment:**
- Use diversity metrics to ensure chemical space coverage
- Check for duplicate or very similar compounds
- Validate against known active compounds if applicable
- Consider follow-up filtering with other tools

## Integration with .bloom* workflows

### Downstream processing

**Virtual screening preparation:**
- Send ZINC compounds directly to DiffDock
- Use for molecular docking campaigns
- Prepare libraries for virtual screening workflows

**Property prediction:**
- Submit to ADMET-AI for comprehensive profiling
- Use DeepSol for solubility prediction
- Generate multi-property datasets

**Compound management:**
- Import into .bloom*'s compound database
- Create focused screening libraries
- Track compound provenance and metadata

### Research applications

**Hit identification:**
- Generate diverse screening libraries
- Create target-focused compound sets
- Design novelty-oriented discovery libraries

**Lead optimization:**
- Find analogs of known active compounds
- Generate focused series for SAR studies
- Identify backup compounds for development

**Method development:**
- Test new screening methodologies
- Benchmark virtual screening tools
- Validate computational chemistry approaches

## Troubleshooting common issues

### No results returned
- Broaden property ranges or remove restrictive filters
- Check subset availability (try different stock categories)
- Simplify substructure queries if too specific
- Verify SMILES/SMARTS syntax

### Poor compound quality
- Enable PAINS and reactivity filters
- Use more restrictive property ranges
- Apply substructure filters for specific chemotypes
- Consider alternative search strategies

### Performance issues
- Reduce requested compound count
- Add more property filters to limit scope
- Use simpler search queries
- Consider batch processing for large requests

### Data interpretation
- Understand subset meanings (in-stock vs. make-on-demand)
- Consider pricing and availability implications
- Review property calculation methods
- Validate against known compounds when possible

## Best practices for ZINC usage

### Search strategy
- Combine property and substructure filters for optimal results
- Save successful search parameters for reproducible queries
- Document search criteria for research reproducibility
- Consider cost vs. diversity trade-offs

### Data management
- Use consistent naming conventions for exported files
- Include metadata about search parameters in file headers
- Version control important compound sets
- Maintain provenance information for research tracking

### Workflow integration
- Plan compound processing pipelines before large searches
- Consider downstream tool requirements when selecting compounds
- Batch process large datasets to manage computational resources
- Automate repetitive search and filtering operations

## Chat Usage

### Example Prompts

- "Find close ZINC analogs of gefitinib"
- "Find close ZINC analogs of gefitinib, then keep MW 200-400 and LogP < 3"
- "Look up ZINC000000000001 and check vendor availability"

### Workflow Chaining

- **Feeds into**: ADMET screening, DiffDock (docking), AiZynthFinder (synthesis), Compound Passport
- **Accepts from**: PubChem (SMILES), REINVENT/GenMol (generated molecules for analog search)

### What Ivy can look up in ZINC22

- **By SMILES**: exact match or close analogs by edit distance
- **By ZINC ID**: SMILES, vendor codes and catalog names
- **By vendor catalog code**: the matching ZINC IDs and SMILES (prices come from a separate vendor price search)

## Read next