BindingDB

The first public molecular recognition database, BindingDB supports research, education and practice in drug discovery, pharmacology and related fields.

BindingDB contains 3.0M data for 1.3M Compounds and 9.5K Targets. Of those, 1.4M data for 673K Compounds and 4.6K Targets were curated by BindingDB curators. BindingDB is a FAIRsharing resource.

If BindingDB was of value to your research, please take a moment to donate to this nonprofit project. Your donation will let us provide you with more data and improved service.

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BindingDB Webinars

BindingDB has started a series of free one-hour webinars designed to be of interest to our users. We aim to host talks by members of the BindingDB team, BindingDB users, and other experts. These events will be held 3-4 times a year and will include plenty of time for open-ended Q&A. We are excited to open this new forum and look forward to meeting many of you!

  • Webinar 1: BindingDB: A Massive, Publicly Accessible, Knowledgebase of Protein-Ligand Binding Data, Mike Gilson, Feb 27, 2025. View:

Recently Added Targets

    1. Serine/threonine-protein kinase greatwall, Human, Q96GX5 (Curated 01/08/25), MASTL: 131 subμM ligands
    2. Phosphodiesterase, Dog, A0A8I3NYE0 (Curated 01/16/25), PDE3A: 88 subμM ligands
    3. ATP-dependent RNA helicase A, Human, Q08211 (Curated 01/28/25), DHX9: 698 subμM ligands
    4. Replicase polyprotein 1a, MERS-CoV, K9N638 (Curated 01/16/25), : 8 subμM ligands
    5. Zinc finger CCCH domain-containing protein 14, Human, Q6PJT7 (Curated 02/22/25), ZC3H14: 1 subμM ligands
    6. 1-deoxy-D-xylulose 5-phosphate reductoisomerase, Staphylococcus hyicus subsp. chromogenes, A0AAE5T299 (Curated 02/24/25), dxr: 3 subμM ligands
    7. 1-deoxy-D-xylulose 5-phosphate reductoisomerase, Staphylococcus schleiferi, A0A7Z7QQH3 (Curated 02/24/25), dxr: 2 subμM ligands
    8. Protoporphyrinogen oxidase, Rough-fruited waterhemp, Q0NZW9 (Curated 02/25/25), PPX2L: 13 subμM ligands
    9. Tafazzin, Human, Q16635 (Curated 01/06/25), TAFAZZIN: 198 subμM ligands
    10. E3 ubiquitin-protein ligase CBL-C, Human, Q9ULV8 (Curated 01/08/25), CBLC: 47 subμM ligands
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Analyze BindingDB data in Google Colab using this Python tool from Pat Walters

This tutorial shows how one can use the BindingDB database and a bit of Python scripting to quickly understand SAR in a pharmaceutical patent. The tutorial covers several patent-related tasks, including accessing BindingDB, exploring chemical scaffolds, performing R-group analyses, and identifying key SAR drivers. 

Coronavirus Binding Data

BindingDB has accelerated collection of COVID related data. You can find the result here.

Try the BindingDB Browser Extension

We are excited to share our new browser extension, BDBFind. Once installed in your browser, BDBFind automatically lets you know when BindingDB has the data from an article, PubMed Entry, or US Patent you are looking at online and provides direct links to view or download the data. Get BDBFind by searching for it in the Chrome webstore or in Firefox extensions or by following these links:

Watch BDBFind in action in this 1.5 minute video: To send feedback about BDBfind, please email us at bindingdb@gmail.com.

BindingDB Data Curation

BindingDB curates US Patents. We have scanned patents back to 2013 for suitable data and are currently up to date as of mid-2020. However, we cannot be sure of capturing all relevant patents, so if you know of a useful one we have missed, please let us know and we will try to curate it. As of March 3, 2025, BindingDB's patent dataset comprises:

  1. Patents: 0
  2. Binding measurements: 0
  3. Compounds: 0
  4. Target proteins: 0
  5. Assays: 0
  6. Average Number of Targets per Patent: NaN

BindingDB curates a set of journals not covered by other public databases. As of March 3, 2025, the status of this curation effort is as follows:

BindingDB is supported by NIH's National Institute of General Medical Sciences (GM070064), and is located at the Skaggs School of Pharmacy and Pharmaceutical Sciences of the University of California San Diego