Establishment of a 3D-structure database for chemical compounds in Indonesian sponges

Retno Prihatiningtyas, Rezi Riadhi Syahdi, Masteria Yunovilsa Putra, Arry Yanuar

Research output: Contribution to journalArticlepeer-review


Objective: Nowadays, There hasn't any three-dimensional (3D) chemical structure database yet for biologically active compound in sponges from Indonesian origin. Therefore, this study aimed to create in silico a 3D-structure database of such compound and to evaluate the preferred software for this purpose. Methods: 2D- structure of selected compounds was established using MarvinSketch software. Conversion from 2D- into 3D-structures was evaluated by comparing MarvinSketch, OpenBabel and VegaZZ software packages. Visualization of the respective 3D-structures was perfomed by using PyMOL software. From 68 scientific articles, 212 chemical compounds were selected from 53 Indonesian sponge species. Results: The conversion of 2D-structures of the selected 212 chemical compound into 3D-structures lead to 7118 files, respectively consisting of 2508 files from the MarvinSketch, 1672 files from the OpenBabel and 1051 files from the VegaZZ software. The results based on the extention files were 1043 SDF, 1258 MOL and 2930 PDB format files of the three-dimensional structure. The valid and correct three-dimensional structure of chemical compound were 914 .sdf format files, 916 format .mol files and 72 .pdb format files. From the three-dimensional structures visualization, the database prefers established by using MarvinSketch with SDF or MOL format files since the results is consistent to literature and contain less number of errors.

Original languageEnglish
Pages (from-to)1211-1218
Number of pages8
JournalPharmacognosy Journal
Issue number6
Publication statusPublished - 1 Jan 2019


  • 2D-and 3D-chemical structures
  • 3D-database of chemical structures
  • Evaluation of software packages
  • Indonesian sponges


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