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
- Three prime repair exonuclease 2, Human, Q9BQ50 (Curated 05/05/25), TREX2: 46 subμM ligands
- Oleoyl-acyl carrier protein thioesterase 1, chloroplastic, Mouse-ear cress, Q42561 (Curated 05/05/25), FATA: 2 subμM ligands
- Heat shock protein 90, Neosartorya fumigata, P40292 (Curated 05/07/25), hsp90: 50 subμM ligands
- Mismatch repair endonuclease PMS2, Human, P54278 (Curated 05/07/25), PMS2: 33 subμM ligands
- Protein enabled homolog, Human, Q8N8S7 (Curated 05/26/25), ENAH: 6 subμM ligands
- Receptor-type tyrosine-protein phosphatase N2, Human, Q92932 (Curated 06/19/25), PTPRN2: 327 subμM ligands
- Cytochrome P450 4F1, Rat, P33274 (Curated 06/05/25), Cyp4f1: 4 subμM ligands
- Cytochrome P450 4A2, Rat, P20816 (Curated 06/05/25), Cyp4a2: 3 subμM ligands
- Diacylglycerol kinase epsilon, Human, P52429 (Curated 06/17/25), DGKE: 87 subμM ligands
- Choline oxidase, Alcaligenes sp, P16101 (Curated 06/17/25), : 118 subμM ligands
- Peroxidase C1A, Horseradish, P00433 (Curated 06/17/25), PRXC1A: 118 subμM ligands
- Ubiquitin-conjugating enzyme E2 D2, Human, P62837 (Curated 06/12/25), UBE2D2: 42 subμM ligands
- Humanin, Human, Q8IVG9 (Curated 05/15/25), MT-RNR2: 14 subμM ligands
- Mitochondrial-derived peptide MOTS-c, Human, A0A0C5B5G6 (Curated 05/15/25), MT-RNR1: 14 subμM ligands
- 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:
- https://chrome.google.com/webstore/search/bdbfind (Once installed, click on the "jigsaw puzzle" icon to keep the BDB icon displayed.)
- https://addons.mozilla.org/addon/bdbfind.
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:
- Patents: 7,942
- Binding measurements: 1,212,173
- Compounds: 599,874
- Target proteins: 2,931
- Assays: 11,313
- 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:
- ACS Chemical Biology 2006-2017 (vol 1-12) data
- ACS BioChemistry 1965-2017 (vol 4-56) data
- Bioorganic Chemistry 1990-2017 (vol 18-73) data
- BMC Chemical Biology 2001-2010 (vol 1-10) data
- ChemBioChem 2001-2017 (vol 2-18) data
- Chemical Biology & Drug Design 2006-2017 (vol 67-89) data
- Chemistry & Biology 1995-2015 (vol 2-22) data
- Journal of Biological Chemistry 1982-2014 (vol 257-289) data
- Journal of Chemical Biology 2010-2010 (vol 3-3) data
- Journal of Enzyme Inhibition and Medicinal Chemistry 2002-2014 (vol 17-29) data
- Nature Chemical Biology 2006-2017 (vol 1-13) data
- Medicinal Chemistry Research 2004-2014 (vol 13-23) data
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