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, 1,417K data for 667K Compounds and 4.6K Targets were curated by BindingDB curators. BindingDB is a FAIRsharing resource.

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Recently Added Targets

    1. Enoyl-[acyl-carrier-protein] reductase [NADH], Acinetobacter baumannii, A0A6F8TJQ1 (Curated 11/08/24), fabI: 4 subμM ligands
    2. Trehalose monomycolate exporter MmpL3, Mycobacterium smegmatis, A0QP27 (Curated 12/14/24), mmpL3: 2 subμM ligands
    3. Macrophage-expressed gene 1 protein, Mouse, A1L314 (Curated 12/18/24), Mpeg1: 2 subμM ligands
    4. Albumin, Crab-eating macaque, A2V9Z4 (Curated 12/17/24), ALB: 1 subμM ligands
    5. UDP-2,3-diacylglucosamine hydrolase, Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578), A6T5R0 (Curated 11/26/24), lpxH: 24 subμM ligands
    6. DNA gyrase subunit B, Escherichia coli, C3SLN3 (Curated 12/13/24), gyrB: 45 subμM ligands
    7. Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2, Human, O00469 (Curated 12/19/24), PLOD2: 3 subμM ligands
    8. Serine/threonine-protein phosphatase with EF-hands 1, Human, O14829 (Curated 12/14/24), PPEF1: 1 subμM ligands
    9. Transcription factor MafG, Human, O15525 (Curated 12/16/24), MAFG: 1 subμM ligands
    10. 4'-phosphopantetheinyl transferase PptT, Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv), O33336 (Curated 12/18/24), pptT: 4 subμM ligands
    11. Neuropilin-2, Human, O60462 (Curated 12/19/24), NRP2: 1 subμM ligands
    12. Diacylglycerol kinase iota, Human, O75912 (Curated 12/18/24), DGKI: 2 subμM ligands
    13. Cdk-related protein kinase 6, malaria parasite P. falciparum, O77239 (Curated 12/17/24), PK6: 67 subμM ligands
    14. Collagen alpha-1(I) chain, Human, P02452 (Curated 12/22/24), COL1A1: 7 subμM ligands
    15. Latent membrane protein 1, HHV-4, P03230 (Curated 12/14/24), LMP1: 1 subμM ligands
    16. Vimentin, Human, P08670 (Curated 12/18/24), VIM: 1 subμM ligands
    17. Small ribosomal subunit protein uS2, Human, P08865 (Curated 12/14/24), RPSA: 1 subμM ligands
    18. CD99 antigen, Human, P14209 (Curated 12/17/24), CD99: 2 subμM ligands
    19. Ras-related C3 botulinum toxin substrate 2, Human, P15153 (Curated 12/14/24), RAC2: 1 subμM ligands
    20. Galectin-1, Mouse, P16045 (Curated 12/18/24), Lgals1: 1 subμM ligands
    21. Heat shock 70 kDa protein 6, Human, P17066 (Curated 12/14/24), HSPA6: 1 subμM ligands
    22. Probable ATP-dependent RNA helicase DDX5, Human, P17844 (Curated 12/21/24), DDX5: 1 subμM ligands
    23. Tumor necrosis factor receptor superfamily member 1B, Human, P20333 (Curated 12/17/24), TNFRSF1B: 1 subμM ligands
    24. Oxysterol-binding protein 1, Human, P22059 (Curated 12/20/24), OSBP: 32 subμM ligands
    25. NKG2-D type II integral membrane protein, Human, P26718 (Curated 12/22/24), KLRK1: 11 subμM ligands
    26. Metalloproteinase inhibitor 3, Human, P35625 (Curated 12/14/24), TIMP3: 8 subμM ligands
    27. Serine/threonine-protein phosphatase 4 catalytic subunit, Human, P60510 (Curated 12/14/24), PPP4C: 1 subμM ligands
    28. Ras-related C3 botulinum toxin substrate 3, Human, P60763 (Curated 12/14/24), RAC3: 2 subμM ligands
    29. Mitogen-activated protein kinase kinase kinase kinase 1, Mouse, P70218 (Curated 12/14/24), Map4k1: 1 subμM ligands
    30. S-adenosylmethionine synthase isoform type-1, Human, Q00266 (Curated 12/19/24), MAT1A: 1 subμM ligands
    31. Xanthine dehydrogenase/oxidase, Mouse, Q00519 (Curated 12/18/24), Xdh: 1 subμM ligands
    32. Inactive tyrosine-protein kinase transmembrane receptor ROR1, Human, Q01973 (Curated 12/18/24), ROR1: 15 subμM ligands
    33. Tyrosine-protein kinase transmembrane receptor ROR2, Human, Q01974 (Curated 12/18/24), ROR2: 4 subμM ligands
    34. Matrilysin, Mouse, Q10738 (Curated 12/20/24), Mmp7: 1 subμM ligands
    35. Interleukin enhancer-binding factor 3, Human, Q12906 (Curated 12/21/24), ILF3: 2 subμM ligands
    36. Mannosyl-oligosaccharide glucosidase, Human, Q13724 (Curated 11/25/24), MOGS: 190 subμM ligands
    37. Cyclin-dependent kinase 12, Mouse, Q14AX6 (Curated 12/18/24), Cdk12: 2 subμM ligands
    38. MHC class I polypeptide-related sequence A, Human, Q29983 (Curated 12/22/24), MICA: 20 subμM ligands
    39. Sigma intracellular receptor 2, Bovine, Q3MHW7 (Curated 12/14/24), TMEM97: 2 subμM ligands
    40. Lysophospholipase-like protein 1, Mouse, Q3UFF7 (Curated 12/21/24), Lyplal1: 1 subμM ligands
    41. Beta-lactamase, Escherichia coli, Q4GY26 (Curated 12/15/24), blaTEM-1: 2 subμM ligands
    42. Retinal dehydrogenase 2, Mouse, Q62148 (Curated 11/21/24), Aldh1a2: 21 subμM ligands
    43. Protein arginine N-methyltransferase 9, Human, Q6P2P2 (Curated 12/19/24), PRMT9: 2 subμM ligands
    44. GDNF family receptor alpha-like, Human, Q6UXV0 (Curated 12/19/24), GFRAL: 2 subμM ligands
    45. ATP-dependent RNA helicase DHX33, Mouse, Q80VY9 (Curated 12/22/24), Dhx33: 2 subμM ligands
    46. Beta-lactamase, Escherichia coli, Q840M4 (Curated 12/15/24), blaCTX-M-27: 1 subμM ligands
    47. threonine--tRNA ligase, Plasmodium falciparum (isolate 3D7), Q8IIA4 (Curated 12/18/24), : 7 subμM ligands
    48. N-acetylaspartylglutamate synthase A, Human, Q8IXN7 (Curated 12/06/24), RIMKLA: 3 subμM ligands
    49. Bifunctional peptidase and arginyl-hydroxylase JMJD5, Human, Q8N371 (Curated 12/19/24), KDM8: 10 subμM ligands
    50. ADP-ribosylation factor GTPase-activating protein 1, Human, Q8N6T3 (Curated 12/14/24), ARFGAP1: 1 subμM ligands
    51. Interleukin-17 receptor E, Human, Q8NFR9 (Curated 12/18/24), IL17RE: 40 subμM ligands
    52. 17-beta-hydroxysteroid dehydrogenase 13, Mouse, Q8VCR2 (Curated 12/22/24), Hsd17b13: 15 subμM ligands
    53. Ryanodine receptor 2, Human, Q92736 (Curated 12/21/24), RYR2: 3 subμM ligands
    54. Crossover junction endonuclease MUS81, Human, Q96NY9 (Curated 12/14/24), MUS81: 2 subμM ligands
    55. Myosin-1, Bovine, Q9BE40 (Curated 11/25/24), MYH1: 112 subμM ligands
    56. Solute carrier family 26 member 6, Human, Q9BXS9 (Curated 12/14/24), SLC26A6: 1 subμM ligands
    57. Melanoma-associated antigen E1, Human, Q9HCI5 (Curated 11/07/24), MAGEE1: 8 subμM ligands
    58. Beta-lactamase, Escherichia coli, Q9L5C7 (Curated 12/15/24), blaCTX-M-14: 3 subμM ligands
    59. Dual oxidase 1, Human, Q9NRD9 (Curated 12/19/24), DUOX1: 1 subμM ligands
    60. N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2, Human, Q9NY97 (Curated 12/17/24), B3GNT2: 36 subμM ligands
    61. Insulin-like growth factor 2 mRNA-binding protein 1, Human, Q9NZI8 (Curated 12/19/24), IGF2BP1: 2 subμM ligands
    62. Zinc finger protein Aiolos, Human, Q9UKT9 (Curated 12/21/24), IKZF3: 11 subμM ligands
    63. DDB1- and CUL4-associated factor 1, Human, Q9Y4B6 (Curated 12/22/24), DCAF1: 6 subμM ligands
    64. HIV-1 protease, Human immunodeficiency virus, Q9YQ30 (Curated 12/19/24), HIV-1 protease: 1 subμM ligands

BindingDB Archive

BindingDB is archived quarterly at UC San Diego Library Digital Collections.

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 December 31, 2024, BindingDB's patent dataset comprises:

  1. Patents: 7,534
  2. Binding measurements: 1,161,587
  3. Compounds: 571,885
  4. Target proteins: 2,792
  5. Assays: 10,739
  6. Average Number of Targets per Patent: 1.90

BindingDB curates a set of journals not covered by other public databases. As of December 31, 2024, the status of this curation effort is as follows:

BindingDB is supported by NIH's National Institute of General Medical Sciences (R24GM144232), and is located at the Skaggs School of Pharmacy and Pharmaceutical Sciences of the University of California San Diego