Chemical Structure Databases in Drug Discovery

Chemical Structure Databases in Drug Discovery

Pramodkumar Pyarelal Gupta (D. Y. Patil University (Deemed), India), Virupaksha Ajit Bastikar (Amity University Mumbai, India) and Santosh Subhash Chhajed (MET Bhujbal Knowledge City, India)
Copyright: © 2019 |Pages: 15
DOI: 10.4018/978-1-5225-7326-5.ch002
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Biologically active and approved molecules have attracted great interest from scientists working in the therapeutic area. This has greatly increased the pressure on the pharma and life science industry in fueling new molecules to the market. Chemical structure database, the backbone of cheminformatics and the bioinformatics industry, has warehoused millions of active and non-active molecules/ligands/derivatives of drug compounds. Numerous public and private chemical databases support the drug discovery projects by contributing their data source in terms of 2D, 3D structure, and annotation reports in development of effective therapeutic projects. In this chapter, the authors discuss important chemical structure databases and their diverse dataset utilization in drug discovery projects.
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ChEMBL is an open source large scale bioactivity database and is publicly available at ( (“ChEMBL,” n.d.-a), reported in Nucleic Acid Research Database Issue in the year 2012 Figure 1. The database largely consists of manually extracted datasets from the medicinal chemistry literature. In-depth data such as compounds structure, biological or physiochemical assays performed for these compounds, the targets from the related assays and other drug discovery related question are addressed. Application of the ChEMBL data includes the suitable chemical tools for target identification, investigation of the off-target drug effects, data mining, construction of predictive modeling for target identification, Identification of bioisostere replacement. In association to literature sources and databases, ChEMBL assimilates bioactivity data and deposited screening results from other public database such as PubChem Bioassay, whereas Dailymed and U.S. Food and Drug Administration (FDA) Orange Book adds a data for the approved drug (Bento et al., 2014). The user can retrieve the data from ChEMBL using Ligand search, target search, browse target, browse drug,browse drug targets and browse drug indications that are listed onto the home page of ChEMBL database Figure 1. In the ligand search option, the user can sketch the drug/ligand structures per their requirement as web based sketching tool is facilitated Figure 1. As well as can search for targets Figure 2 (“ChEMBL,” n.d.-a). It has 2,101,843 compound records, 1,735,442 compounds (of which 1,727,112 have mol files), 14,675,320 activities, 1,302,147 assays, 11,538 targets and 67,722 documents Table 1 (“ChEMBL,” n.d.-b)

Figure 1.

Home page ChEMBL database,


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