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 9.6K Targets. Of those, 1.5M data for 695K Compounds and 4.7K 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 2: 8:00 am California time, September 17, 2025: Synergies between BindingDB and PubChem. Dr. Christopher Southan, Honorary Professor, Deanery of Biomedical Sciences, University of Edinburgh (Note date change from September 18 to 17). Please register at https://uchealth.zoom.us/webinar/register/WN_5OphMlPQQu-1gNuhHkLsGQ
  • Webinar 1: BindingDB: A Massive, Publicly Accessible, Knowledgebase of Protein-Ligand Binding Data, Mike Gilson, Feb 27, 2025. View:

Recently Added Targets

    1. Three prime repair exonuclease 2, Human, Q9BQ50 (Curated 05/05/25), TREX2: 46 subμM ligands
    2. Oleoyl-acyl carrier protein thioesterase 1, chloroplastic, Mouse-ear cress, Q42561 (Curated 05/05/25), FATA: 2 subμM ligands
    3. Heat shock protein 90, Neosartorya fumigata, P40292 (Curated 05/07/25), hsp90: 50 subμM ligands
    4. Mismatch repair endonuclease PMS2, Human, P54278 (Curated 05/07/25), PMS2: 33 subμM ligands
    5. Protein enabled homolog, Human, Q8N8S7 (Curated 05/26/25), ENAH: 6 subμM ligands
    6. Receptor-type tyrosine-protein phosphatase N2, Human, Q92932 (Curated 06/19/25), PTPRN2: 327 subμM ligands
    7. Cytochrome P450 4F1, Rat, P33274 (Curated 06/05/25), Cyp4f1: 4 subμM ligands
    8. Cytochrome P450 4A2, Rat, P20816 (Curated 06/05/25), Cyp4a2: 3 subμM ligands
    9. Diacylglycerol kinase epsilon, Human, P52429 (Curated 06/17/25), DGKE: 87 subμM ligands
    10. Choline oxidase, Alcaligenes sp, P16101 (Curated 06/17/25), : 118 subμM ligands
    11. Peroxidase C1A, Horseradish, P00433 (Curated 06/17/25), PRXC1A: 118 subμM ligands
    12. Ubiquitin-conjugating enzyme E2 D2, Human, P62837 (Curated 06/12/25), UBE2D2: 42 subμM ligands
    13. Humanin, Human, Q8IVG9 (Curated 05/15/25), MT-RNR2: 14 subμM ligands
    14. Mitochondrial-derived peptide MOTS-c, Human, A0A0C5B5G6 (Curated 05/15/25), MT-RNR1: 14 subμM ligands
    15. Apolipoprotein B receptor, Human, Q0VD83 (Curated 06/11/25), APOBR: 7 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 June 30, 2025, BindingDB's patent dataset comprises:

  1. Patents: 7,942
  2. Binding measurements: 1,212,173
  3. Compounds: 599,874
  4. Target proteins: 2,931
  5. Assays: 11,313
  6. Average Number of Targets per Patent: 1.90

BindingDB curates a set of journals not covered by other public databases. As of June 30, 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