Cheminformatic Tools and Databases for Pharmacology
e-Drug3D offers a facility to explore FDA approved drugs and active metabolites (see the description).

2028 molecular structures approved between 1939 and 2021 with a molecular weight ≤ 2000 have been registered (last update: July 2021).



References:

  • Data sets representative of the Structures and Experimental Properties of FDA-approved Drugs, Douguet D., ACS Med Chem Lett., 2018, 9(3):204-209. doi: 10.1021/acsmedchemlett.7b00462

  • Pihan E., Colliandre L., Guichou J.-F. and Douguet D., e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design, Bioinformatics, 2012, 28(11):1540-1541. doi: 10.1093/bioinformatics/bts186

  • ZENODO doi: 10.5281/zenodo.4432352

Last registration

July, 7, 2021

SG3199





Download Data sets:
  • Chemical Structures (component 1/4):


  • Pharmacodynamics (component 2/4)

    • Download the e-Drug3D-PD data set in text format. Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, Primary target, ATC code(s), PDB codes and the Unified Set of drug Targets extracted from DrugCentral (DrugCentral).


  • Pharmacokinetics (component 3/4)

    • Display metabolite groups (drugs and active metabolites belonging to the same family have been gathered in the same group. Thus, a structure is either a mother or an offspring of another one)

    • Download the e-Drug3D-PK data set in text format. Column/field value is separated by a semicolon. It contains the e-Drug3D ID, INN (drug name), CAS number, year of approval, Status, is_or_has a metabolite, routes of administration, Volume of distribution (VD), Clearance (Cl), Plasma Protein Binding (PPB), Half-life (t1/2), Bioavailability (F), Cmax/Tmax, comment on solubility.


  • FDA Registration Data (component 4/4)

    • Download the e-Drug3D-RD data set in text format. Column/field value is separated by a semicolon. It contains the ID, name (INN), CAS number, First year of approval, Status, KNApSAcK Id if natural product, all associated NDA numbers [FDA approval number, name of the label file in PDF format, company name, year of approval and commercial name of the drug] and the Indication/Therapeutic class information

    • Download the drug label files in PDF format (compressed directory). A label file is named with the NDA number. The NDA number is the approval number assigned by the FDA. A drug may possess several NDA numbers (see the above e-Drug3D-RD data set)

    • The following file contains the list of discarded NDA numbers (biologics, contrast agents...)


Database content:

Drug names (INN) are listed below:

They have been gathered in function of the year of the first approval in decreasing order.

The name of the company that launched it is given in parentheses.

Dxxxx is the identifier of the drug in our database.

'M' in front of a name means that the compound is (an active) METABOLITE (at bottom of the list).

The year 0 lists drugs without any defined year (mainly withdrawn or discontinued drugs but with valid NDA agreement number)


Browse Drug names (INN) in function of the year of the first approval: list.html

Browse Drug names (INN) in alphabetical order: list.html





Description of the database:


  • e-Drug3D mirrors the current content of the U.S. pharmacopeia of small drugs (molecular weight ≤ 2000). Discarded NDA/Approved Drugs (biologics, contrast agents...) are listed at this link.

  • e-Drug3D uses the 'Drugs@FDA Data File' (http://www.fda.gov/Drugs/InformationOnDrugs/ucm079750.htm) released by the FDA to construct and update the database.

  • The structure of each drug has been manually checked to assign the exact stereochemistry to chiral centers (enantiomers are different structures and are registered as such). Chemical structures have been extracted from drug labels and checked using the SciFinder/CAS database.

  • Active metabolites have been registered with the prefix "M " (except if the active metabolite structure has been approved under another name or possesses an INN).

  • FDA registration data are provided with a link to the FDA website.

  • Pharmacokinetic data has been extracted from the drug label (additional sources are the review by Obach R.S. et al. (Drug Metabolism and Disposition, 2008, 36(7), 1385-1405), DailyMed (U.S. National Library of Medicine), Drugs.com, VIDAL and PubMed).

  • Pharmacodynamic data (Primary target) has been extracted from the drug label (additional sources are PubMed).

  • A link to the Anatomical Therapeutic Chemical (ATC) classification system (World Health Organization) is provided when it exists.

  • Physicochemical properties have been calculated.

  • Chemistry information and links to patents, synthesis references and commercial suppliers are indicated.

  • Shape similarities between drugs have been calculated and a superimposition display is available.




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