BindingDB Download

Fetch BindingDB ligand and binding metadata files for protein-ligand records.

Input

Entry ID

Database

Output

Configure inputs to begin

Set options on the left, then click “Fetch downloads” — or start from an example.

50000007

50361334

50127775

How to download BindingDB records?

BindingDB Download fetches BindingDB ligand and binding metadata by BindingDB monomer ID. It returns the available record file and summarizes ligand, target, affinity, SMILES, PubMed, and DOI metadata when those fields are available.

Use this tool when you need binding records for protein-ligand analysis, assay review, ligand metadata, or reproducible references for bioactivity data.

Input	Description
`Entry ID`	BindingDB monomer identifier. Examples: `50000007`, `50361334`, `50127775`.

Setting	Description
`Database`	Opens the selected database download tool.

Supported BindingDB downloads

File	Format	Use
JSON	`.json`	BindingDB record link and associated binding metadata.

Understanding the results

The results panel lists the available BindingDB file link. The Details tab summarizes the database, BindingDB ID, record title, file label, format, source type, filename, and URL.

Filenames follow the pattern:

Text

bindingdb-50000007-json.json

BindingDB search results can contain richer assay context than a direct monomer lookup. Use /app/databases when you need to discover records from a target, PDB ID, UniProt accession, or SMILES query.

Common use cases

Store binding record links with docking or screening outputs.
Cross-reference ligand IDs with affinity measurements.
Capture BindingDB identifiers before ligand preparation.
Keep target and publication metadata near downstream analysis results.

FAQ

What identifier should I enter?

Use a BindingDB monomer ID for direct downloads. If you only know a target or ligand structure, search BindingDB first and then download the selected record.

Does this calculate affinity?

No. The tool retrieves available BindingDB record metadata. It does not estimate binding affinity.

Can I use the SMILES metadata for ligand workflows?

Yes, when SMILES is present in the record metadata. For structure conversion, use Open Babel or related ligand conversion tools.

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