BindingDB logo
myBDB logout

Please try our new beta-test BindingDB site!

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of September 18, 2021, BindingDB contains 41,296 Entries, each with a DOI, containing 2,338,906 binding data for 8,617 protein targets and 1,011,134 small molecules.

There are 2823 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 8263 crystal structures allowing proteins to 85% sequence identity.

You can also use BindingDB data through the Registry of Open Data on AWS: https://registry.opendata.aws/binding-db.

Simple Search
Article Titles, Authors, Assays, Compound Names, Target Names

Use ? for single-letter wild-card or * for general wild-card.
For example, "adeny*" or "adeny?". Query cannot start with wild card.
Advanced Search Combine multiple search criteria, such as chemical structures, target names, and numerical affinities; restrict searches by data source, such as BindingDB, ChEMBL, PubChem, and Patents.
Messages
  1. Recently added Targets
    1. UDP-3-O-acyl-N-acetylglucosamine deacetylase, Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578), A6T4N9 (Curated 07/25/21), lpxC: 3 subμM ligands
    2. Sodium channel subunit beta-2, Human, O60939 (Curated 08/13/21), SCN2B: 17 subμM ligands
    3. Ataxin-2, Mouse, O70305 (Curated 08/12/21), Atxn2: 6 subμM ligands
    4. Protein phosphatase 1 regulatory subunit 15A, Human, O75807 (Curated 08/14/21), PPP1R15A: 1 subμM ligands
    5. DNA (cytosine-5)-methyltransferase 3A, Mouse, O88508 (Curated 08/13/21), Dnmt3a: 1 subμM ligands
    6. Complement factor B, Mouse, P04186 (Curated 08/12/21), Cfb: 6 subμM ligands
    7. Thrombospondin-1, Human, P07996 (Curated 08/13/21), THBS1: 14 subμM ligands
    8. S-formylglutathione hydrolase, Human, P10768 (Curated 08/13/21), ESD: 1 subμM ligands
    9. Beta-glucuronidase, Mouse, P12265 (Curated 08/12/21), Gusb: 1 subμM ligands
    10. Diacylglycerol kinase alpha, Human, P23743 (Curated 08/13/21), DGKA: 4 subμM ligands
    11. Carbamoyl-phosphate synthase [ammonia], mitochondrial, Human, P31327 (Curated 08/13/21), CPS1: 7 subμM ligands
    12. Stress-70 protein, mitochondrial, Human, P38646 (Curated 08/12/21), HSPA9: 5 subμM ligands
    13. Phospholipase A and acyltransferase 3, Human, P53816 (Curated 08/13/21), PLAAT3: 16 subμM ligands
    14. Sodium channel subunit beta-1, Mouse, P97952 (Curated 08/13/21), Scn1b: 1 subμM ligands
    15. Programmed cell death protein 1, Mouse, Q02242 (Curated 08/13/21), Pdcd1: 1 subμM ligands
    16. TAR DNA-binding protein 43, Human, Q13148 (Curated 08/14/21), TARDBP: 2 subμM ligands
    17. Collagenase ColH, Hathewaya histolytica, Q46085 (Curated 08/13/21), colH: 3 subμM ligands
    18. Sodium channel subunit beta-2, Mouse, Q56A07 (Curated 08/13/21), Scn2b: 13 subμM ligands
    19. Protein phosphatase 1 regulatory subunit 15B, Human, Q5SWA1 (Curated 08/14/21), PPP1R15B: 1 subμM ligands
    20. Sodium channel protein type 9 subunit alpha, Mouse, Q62205 (Curated 12/17/16), Scn9a: 52 subμM ligands
    21. BTB/POZ domain-containing protein KCTD11, Human, Q693B1 (Curated 08/12/21), KCTD11: 1 subμM ligands
    22. Fatty acid 2-hydroxylase, Human, Q7L5A8 (Curated 09/06/21), FA2H: 57 subμM ligands
    23. Structural polyprotein, CHIKV, Q8JUX5 (Curated 07/25/21), : 3 subμM ligands
    24. Interleukin-1 receptor-associated kinase 4, Mouse, Q8R4K2 (Curated 08/13/21), Irak4: 1 subμM ligands
    25. Phospholipase A and acyltransferase 5, Human, Q96KN8 (Curated 08/13/21), PLAAT5: 28 subμM ligands
    26. Serine/threonine-protein kinase LMTK3, Human, Q96Q04 (Curated 08/13/21), LMTK3: 6 subμM ligands
    27. TSC22 domain family protein 3, Human, Q99576 (Curated 07/25/21), TSC22D3: 21 subμM ligands
    28. Programmed cell death 1 ligand 2, Human, Q9BQ51 (Curated 08/15/21), PDCD1LG2: 313 subμM ligands
    29. Programmed cell death 1 ligand 1, Mouse, Q9EP73 (Curated 08/13/21), Cd274: 2 subμM ligands
    30. Toll-like receptor 9, Mouse, Q9EQU3 (Curated 08/13/21), Tlr9: 1 subμM ligands
    31. N-alpha-acetyltransferase 50, Human, Q9GZZ1 (Curated 08/13/21), NAA50: 12 subμM ligands
    32. OXA23 carbapenemase, Acinetobacter baumannii, Q9L4P2 (Curated 08/13/21), ari-1: 1 subμM ligands
    33. Phospholipase A and acyltransferase 2, Human, Q9NWW9 (Curated 08/13/21), PLAAT2: 10 subμM ligands
    34. Phospholipase A and acyltransferase 4, Human, Q9UL19 (Curated 08/13/21), PLAAT4: 10 subμM ligands
  2. 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.
Patent Curation
by BindingDB

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 September 18, 2021, BindingDB's patent dataset comprises:

  1. Patents: 5,025
  2. Binding measurements: 748,866
  3. Compounds: 375,047
  4. Target proteins: 2,118
  5. Assays: 7,278
  6. Average Number of Targets per Patent: 1.92

Journal Curation
by BindingDB
BindingDB continually curates a set of journals not covered by other public databases. As of September 18, 2021, the status of our current curation effort is as follows:
  1. ACS Chemical Biology 2006-2017 (vol 1-12) magnifying glass
  2. ACS BioChemistry 1965-2017 (vol 4-56) magnifying glass
  3. Bioorganic Chemistry 1990-2017 (vol 18-73) magnifying glass
  4. BMC Chemical Biology 2001-2010 (vol 1-10) magnifying glass
  5. ChemBioChem 2001-2017 (vol 2-18) magnifying glass
  6. Chemical Biology & Drug Design 2006-2017 (vol 67-89) magnifying glass
  7. Chemistry & Biology 1995-2015 (vol 2-22) magnifying glass
  8. Journal of Biological Chemistry 1982-2014 (vol 257-289) magnifying glass
  9. Journal of Chemical Biology 2010-2010 (vol 3-3) magnifying glass
  10. Journal of Enzyme Inhibition and Medicinal Chemistry 2002-2014 (vol 17-29) magnifying glass
  11. Nature Chemical Biology 2005-2017 (vol 1-13) magnifying glass
  12. Medicinal Chemistry Research 2004-2014 (vol 13-23) magnifying glass
  1. PubMed IDs: 3,459
  2. Binding measurements: 111,369
  3. Compounds: 46,289
  4. Target proteins: 2,997
  5. Assays: 3,254
myBDB
Username Password
logout Username is your registered email in BindingDB.register
Video Tutorials
  1. Get all data from an article
  2. Download all data for a target of interest
  3. Find and view all data for a target of interest
  4. Find my compound's targets