AroCageDB: A Web-Based Resource for Aromatic Cage Binding Sites and Their Intrinsic Ligands

Jianyu Li; Aurélien F A Moumbock; Ammar Qaseem; Qianqing Xu; Yue Feng; Dan Wang; Stefan Günther

doi:10.1021/acs.jcim.1c00927

AroCageDB: A Web-Based Resource for Aromatic Cage Binding Sites and Their Intrinsic Ligands

J Chem Inf Model. 2021 Nov 22;61(11):5327-5330. doi: 10.1021/acs.jcim.1c00927. Epub 2021 Nov 5.

Authors

Jianyu Li¹, Aurélien F A Moumbock¹, Ammar Qaseem¹, Qianqing Xu¹, Yue Feng¹, Dan Wang¹, Stefan Günther¹

Affiliation

¹ Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany.

PMID: 34738791
DOI: 10.1021/acs.jcim.1c00927

Abstract

While aromatic cages have extensively been investigated in the context of structural biology, molecular recognition, and drug discovery, there exist to date no comprehensive resource for proteins sharing this conserved structural motif. To this end, we parsed the Protein Data Bank and thus constructed the Aromatic Cage Database (AroCageDB), a database for investigating the binding pocket descriptors and ligand binding space of aromatic-cage-containing proteins (ACCPs). AroCageDB contains 487 unique ACCPs bound to 890 unique ligands, for a total of 1636 complexes. This web-accessible database provides a user-friendly interface for the interactive visualization of ligand-bound ACCP structures, with a variety of search options that will open up opportunities for structural analyses and drug discovery campaigns. AroCageDB is freely available at http://www.pharmbioinf.uni-freiburg.de/arocagedb/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Databases, Protein
Internet*
Ligands
Proteins*
User-Computer Interface

Substances

Ligands
Proteins