The ZINC (ZINC Is Not Commercial) database is a publicly accessible collection of commercially available chemical compounds prepared for use in virtual screening and drug discovery. It is maintained by the Irwin and Shoichet labs at the University of California, San Francisco (UCSF) and is widely utilized by researchers in computational chemistry, medicinal chemistry, and related fields.
Purpose and Scope
- Provides three‐dimensional (3‑D) structures of small molecules in multiple file formats (e.g., .mol2, .sdf, .pdbqt).
- Supplies associated physicochemical properties, such as molecular weight, calculated logP, hydrogen‑bond donors/acceptors, and rotatable bond counts.
- Links each entry to the commercial vendor(s) that sell the compound, allowing users to obtain physical samples for experimental testing.
Content
- As of 2024, the database contains over 200 million unique compounds, covering a broad chemical space that includes drug‑like, lead‑like, and fragment‑like molecules.
- Subsets are curated for specific screening strategies (e.g., “drug‑like,” “lead‑like,” “fragment‑like,” “protease‑focused,” “natural products”).
Access and Usage
- The database can be searched and downloaded through the ZINC web portal (zinc15.docking.org) without registration; bulk downloads and API access may require a free account.
- Users can filter compounds by physicochemical criteria, structural similarity, vendor, price, and other attributes.
- ZINC provides ready‑to‑use input files compatible with popular docking programs such as AutoDock Vina, DOCK, and Glide.
Historical Development
- Launched in 2005 as “ZINC 1.0,” the resource has undergone multiple revisions, expanding the number of compounds and improving data quality.
- The “ZINC15” release introduced a modern interface, enhanced metadata, and the ability to generate on‑the‑fly conformer libraries.
Impact
- ZINC is cited in thousands of scientific publications as a source of virtual screening libraries.
- It facilitates rapid hypothesis testing by enabling researchers to perform large‑scale in‑silico screens against target proteins before committing resources to synthesis or purchase.
Limitations
- The database reflects the availability of compounds at the time of indexing; vendor stock status may change, requiring users to verify current availability.
- While extensive, ZINC does not include all possible chemical entities, and certain proprietary or custom‑synthesized molecules are absent.
Related Resources
- PubChem (NCBI) – another large repository of chemical information.
- ChEMBL – focuses on bioactivity data for known compounds.
- ChemSpider – aggregates chemical structures from multiple sources.
The ZINC database remains a cornerstone resource for computational screening workflows, offering a large, well‑annotated, and vendor‑linked collection of small molecules for drug discovery research.
