NDLI: Identification of ligand binding site on RXRγ using molecular docking and dynamics methods

Content Provider	Springer Nature Link
Author	Zhao, Peng Liao, Qing hua Ren, Cheng Feng Wei, Jing
Copyright Year	2010
Abstract	Retinoid X receptors (RXRα, β and γ) are recently known to be cancer chemotherapies targets. The ligand binding domains of RXRs have been crystallized, but the information of RXRγ ligand binding site is not yet available due to the lack of liganded complex. A thorough understanding of the ligand binding sites is essential to study RXRs and may result in cancer therapeutic breakthrough. Thus we aimed to study the RXRγ ligand binding site and find out the differences between the three subtypes. Alignment and molecular simulation were carried out for identifying the RXRγ ligand binding site, characterizing the RXRγ ligand binding mode and comparing the three RXRs. The result has indicated that the RXRγ ligand binding site is defined by helices H5, H10, β-sheet s1 and the end loop. Besides hydrophobic interactions, the ligand 9-cis retinoic acid interacts with RXRγ through a hydrogen bond with Ala106, a salt bridge with Arg95 and the π-π interactions with Phe217 and Phe218. The binding modes exhibit some similarities among RXRs, such as the interactions with Arg95 and Ala106. Nonetheless, owing to the absence of Ile47, Cys48, Ala50, Ala51 and residues 225∼237 in the active site, the binding pocket in RXRγ is two times larger than those of RXRα and RXRβ. Meanwhile, spatial effects of Trp84, Arg95, Ala106, Phe217 and Phe218 help to create a differently shaped binding pocket as compared to those of RXRα and RXRβ. Consequently, the ligand in RXRγ undergoes a “standing” posing which is distinct from the other two RXRs.
Starting Page	1259
Ending Page	1265
Page Count	7
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	17
Issue Number	6
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-08-26
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	9-cis retinoic acid Ligand binding site Molecular docking Molecular dynamics simulation Retinoid X receptor Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Life Sciences Health Informatics Biomedicine general
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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