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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 August 28, 2022, BindingDB contains 41,296 Entries, each with a DOI, containing 2,588,694 binding data for 8,912 protein targets and 1,112,245 small molecules.

There are 5,988 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 11,442 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.

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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. Glucan 1,4-alpha-glucosidase, Shiitake mushroom, A0A1Q3E5G6 (Curated 07/21/22), : 3 subμM ligands
    2. Lys-gingipain, Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561), B2RLK2 (Curated 08/21/22), kgp: 99 subμM ligands
    3. Neuraminidase, Influenza A virus (strain A/WS/1933 H1N1), B4URF0 (Curated 08/24/22), NA: 12 subμM ligands
    4. Polymerase basic protein 2, Influenza A virus (strain A/WS/1933 H1N1), B4URF7 (Curated 08/06/22), PB2: 345 subμM ligands
    5. Hsp90 chaperone protein kinase-targeting subunit, Filobasidiella neoformans, F5H9H0 (Curated 08/06/22), : 93 subμM ligands
    6. Beta-hexosaminidase, Bovine, H7BWW2 (Curated 08/24/22), HEXB: 7 subμM ligands
    7. Hydroxyacid oxidase 1, Pig, I3LVF1 (Curated 08/22/22), HAO1: 1 subμM ligands
    8. Stanniocalcin-1, Mouse, O55183 (Curated 08/25/22), Stc1: 3 subμM ligands
    9. Proteinase-activated receptor 4, Mouse, O88634 (Curated 08/24/22), F2rl3: 12 subμM ligands
    10. Immunoglobulin lambda variable 6-57, Human, P01721 (Curated 08/23/22), IGLV6-57: 25 subμM ligands
    11. Envelope phospholipase F13, VACV, P04021 (Curated 08/24/22), : 5 subμM ligands
    12. Eukaryotic translation initiation factor 2 subunit 1, Human, P05198 (Curated 08/20/22), EIF2S1: 21 subμM ligands
    13. Interleukin-3, Human, P08700 (Curated 07/21/22), IL3: 4 subμM ligands
    14. Replicase polyprotein 1a, 2019-nCoV, P0DTC1 (Curated 08/15/22), : 134 subμM ligands
    15. Calcitonin gene-related peptide 2, Human, P10092 (Curated 08/20/22), CALCB: 23 subμM ligands
    16. Islet amyloid polypeptide, Human, P10997 (Curated 08/23/22), IAPP: 4 subμM ligands
    17. Alpha-1-antitrypsin-related protein, Human, P20848 (Curated 08/24/22), SERPINA2: 1 subμM ligands
    18. Lon protease homolog, mitochondrial, Human, P36776 (Curated 08/20/22), LONP1: 20 subμM ligands
    19. Sterol regulatory element-binding protein 1, Human, P36956 (Curated 08/20/22), SREBF1: 2 subμM ligands
    20. Heat shock protein 90 homolog, Yeast, P46598 (Curated 08/06/22), HSP90: 37 subμM ligands
    21. Dual specificity mitogen-activated protein kinase kinase 4, Mouse, P47809 (Curated 08/19/22), Map2k4: 4 subμM ligands
    22. Stanniocalcin-1, Human, P52823 (Curated 08/25/22), STC1: 3 subμM ligands
    23. Tyrosine-protein kinase receptor UFO, Mouse, Q00993 (Curated 08/21/22), Axl: 32 subμM ligands
    24. Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase, Rat, Q09326 (Curated 08/25/22), Mgat2: 3 subμM ligands
    25. Gastric inhibitory polypeptide receptor, Mouse, Q0P543 (Curated 08/18/22), Gipr: 2 subμM ligands
    26. Beta-hexosaminidase subunit alpha, Bovine, Q0V8R6 (Curated 08/24/22), HEXA: 1 subμM ligands
    27. E3 ubiquitin-protein ligase CBL-B, Human, Q13191 (Curated 08/20/22), CBLB: 1 subμM ligands
    28. Glycine N-methyltransferase, Human, Q14749 (Curated 08/24/22), GNMT: 5 subμM ligands
    29. Transient receptor potential cation channel subfamily M member 1, Mouse, Q2TV84 (Curated 08/23/22), Trpm1: 1 subμM ligands
    30. Serine/threonine-protein kinase TNNI3K, Mouse, Q5GIG6 (Curated 08/24/22), Tnni3k: 1 subμM ligands
    31. Tyrosine-protein kinase, Rat, Q5S255 (Curated 08/20/22), Btk: 1 subμM ligands
    32. Tyrosine-protein kinase Mer, Mouse, Q60805 (Curated 08/21/22), Mertk: 30 subμM ligands
    33. N6-adenosine-methyltransferase catalytic subunit, Human, Q86U44 (Curated 08/22/22), METTL3: 6 subμM ligands
    34. Hepatitis A virus cellular receptor 2, Human, Q8TDQ0 (Curated 08/25/22), HAVCR2: 10 subμM ligands
    35. Three-prime repair exonuclease 1, Mouse, Q91XB0 (Curated 08/01/22), Trex1: 16 subμM ligands
    36. Mitogen-activated protein kinase 8, Mouse, Q91Y86 (Curated 08/24/22), Mapk8: 8 subμM ligands
    37. F-box/WD repeat-containing protein 5, Human, Q969U6 (Curated 08/07/22), FBXW5: 23 subμM ligands
    38. Interleukin-17 receptor A, Human, Q96F46 (Curated 07/21/22), IL17RA: 190 subμM ligands
    39. Proline-rich acidic protein 1, Human, Q96NZ9 (Curated 08/23/22), PRAP1: 6 subμM ligands
    40. Protein orai-2, Human, Q96SN7 (Curated 08/23/22), ORAI2: 1 subμM ligands
    41. Bifunctional polynucleotide phosphatase/kinase, Human, Q96T60 (Curated 08/15/22), PNKP: 66 subμM ligands
    42. Calcium and integrin-binding protein 1, Human, Q99828 (Curated 08/22/22), CIB1: 25 subμM ligands
    43. Carboxypeptidase B2, Rat, Q9EQV9 (Curated 08/23/22), Cpb2: 2 subμM ligands
    44. Serine/threonine-protein kinase/endoribonuclease IRE1, Mouse, Q9EQY0 (Curated 08/19/22), Ern1: 1 subμM ligands
    45. Presenilins-associated rhomboid-like protein, mitochondrial, Human, Q9H300 (Curated 08/22/22), PARL: 2 subμM ligands
    46. Pannexin-1, Mouse, Q9JIP4 (Curated 08/23/22), Panx1: 3 subμM ligands
    47. Transient receptor potential cation channel subfamily M member 5, Mouse, Q9JJH7 (Curated 08/20/22), Trpm5: 4 subμM ligands
    48. Probable G-protein coupled receptor 27, Human, Q9NS67 (Curated 08/23/22), GPR27: 8 subμM ligands
    49. Three-prime repair exonuclease 1, Human, Q9NSU2 (Curated 08/01/22), TREX1: 26 subμM ligands
    50. Apelin receptor, Mouse, Q9WV08 (Curated 08/24/22), Aplnr: 23 subμM ligands
  2. BindingDB has accelerated collection of COVID related data. You can find the result here.
  3. 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 August 28, 2022, BindingDB's patent dataset comprises:

  1. Patents: 5,866
  2. Binding measurements: 904,846
  3. Compounds: 437,875
  4. Target proteins: 2,321
  5. Assays: 8,481
  6. Average Number of Targets per Patent: 1.91
Journal Curation
by BindingDB		 BindingDB continually curates a set of journals not covered by other public databases. As of August 28, 2022, 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: 3,467
  2. Binding measurements: 112,812
  3. Compounds: 47,154
  4. Target proteins: 2,991
  5. Assays: 3,268
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