| Literature DB >> 27789690 |
Oleg Ursu1, Jayme Holmes1, Jeffrey Knockel2, Cristian G Bologa1, Jeremy J Yang1, Stephen L Mathias1, Stuart J Nelson1, Tudor I Oprea3.
Abstract
DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.Entities:
Mesh:
Substances:
Year: 2016 PMID: 27789690 PMCID: PMC5210665 DOI: 10.1093/nar/gkw993
Source DB: PubMed Journal: Nucleic Acids Res ISSN: 0305-1048 Impact factor: 16.971
Figure 1.DrugCentral main entities and relations diagram. Active pharmaceutical ingredients' is the central bridge entity that serves as a to link to the other database entities.
DrugCentral database entities and statistics
| Entities (Annotated APIs) | |
|---|---|
| 4444 | |
| FDA drugs | 2021 |
| Drugs approved outside US | 2423 |
| Small molecules | 3799 |
| Salts and inorganic molecules | 112 |
| Biologics and peptides | 239 |
| Other drugs | 294 |
| Parent molecules | 199 (308) |
| 837 (1689) | |
| Human protein targets | 600 (1387) |
| Infectious agents targets | 194 (221) |
| Metabolites & biopolymers | 43 (89) |
| Protein–drug crystal complex (PDB) | 48 (82) |
| 1452 (283) | |
| 13 825 (1792) | |
| Human proteins | 10 427 (1605) |
| Other species | 3398 (1002) |
| WHO ATC code | 4195 (2941) |
| FDA Established Pharmacologic Class | 428 (1165) |
| MeSH pharmacological action | 424 (2529) |
| ChEBI ontology roles | 285 (1487) |
| 2224 (2247) | |
| 1458 (1376) | |
| 847 (646) | |
| 67 064 (1660) | |
| Rx pharmaceutical products | 29 665 (1561) |
| OTC pharmaceutical products | 37 399 (286) |
| 61 349 (4444) | |
| CAS registry number | 6072 (4444) |
| PubChem Compound Id | 4175 (4175) |
| FDA Unique Ingredient Identifier (UNII) | 4304 (4304) |
| ChEMBL-db id | 5615 (4075) |
| WHO INN id | 3519 (3519) |
| SNOMED-CT | 4745 (2637) |
| KEGG DRUG | 3501 (3501) |
| NDFRT | 4171 (2406) |
| RxNorm RxCUI | 2897 (2897) |
| IUPHAR/BPS ligand id | 1345 (1345) |
| UMLS CUI | 2839 (2839) |
| CHEBI | 2557 (2557) |
| MeSH | 4063 (3846) |
| DrugBank | 2473 (2388) |
| Protein databank ligand id | 646 (618) |
Structure overlap between 3935 DrugCentral structures (MOL V2000 subset) and other small molecule drug databases. The upper triangle (blue) summarizes the APIs overlap calculated using stereo chemistry information. The lower triangle (orange) contains overlaps determined with stereochemistry omitted. The Diagonal entries represent number of unique molecular structure records before and after removal of salt/solvent, or invalid/duplicate records.
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Distribution of Ro5 criteria and related physicochemical properties for the orally formulated drugs subset of DrugCentral
| Property | Min | 1st quantile | Median | 3rd quantile | Max |
|---|---|---|---|---|---|
| MW | 75.07 | 262.22 | 324.8 | 411.49 | 1526.74 |
| cLogP | −8.17 | 0.94 | 2.43 | 4.05 | 20.43 |
| HAC | 0 | 3 | 5 | 7 | 36 |
| HDO | 0 | 1 | 1 | 2 | 19 |
| Ro5 | 0 | 0 | 0 | 0 | 4 |
| ROTB | 0 | 3 | 4 | 7 | 31 |
| RGB | 0 | 12 | 17 | 21 | 74 |
| Rings | 0 | 2 | 3 | 4 | 10 |
| Rings Aro | 0 | 1 | 2 | 2 | 6 |
| Rings Aliph | 0 | 0 | 1 | 2 | 9 |
| TPSA | 0 | 40.73 | 67.2 | 98.78 | 573.91 |
MW - molecular weight; cLogP - estimated log octanol/water partition coefficient (CLOGP, BioByte); HAC - hydrogen bond acceptors; HDO - hydrogen bond donors; Ro5 - rule of 5 violations; ROTB - rotatable bonds; RGB - rigid bonds; Rings - smallest set of smallest rings (SSSR); Rings Aro - aromatic rings; Rings Aliph - aliphatic rings; TPSA - topological polar surface area (Å2).
Commercial drug collections overlap with FDA small molecules drugs subset (1608 structures)
| Total number of chemicals | FDA small molecule drugs overlap with stereochemistry specified (%) | FDA small molecule drugs overlap with stereochemistry omitted (%) | URL | |
|---|---|---|---|---|
| Prestwick Chemical Library | 1280 | 740 (46%) | 824 (51%) | |
| Selleckchem FDA-approved Drug Library | 978 | 595 (37%) | 670 (42%) | |
| MicroSource Discovery US Drug Collection | 1385 | 687 (43%) | 929 (58%) | |
| eMolecules | 8 129 798 | 1208 (75%) | 1313 (82%) |
Figure 2.DrugCentral drug report page: (A) description, structure, properties and synonyms; (B) drug dosage, regulatory approvals and pharmacological action; (C) drug indications, contra-indications and off-label uses; (D) links to external resources; (E) bioactivity profile and mechanism of action target(s); (F) FDA approval pharmaceutical products containing API.