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InChI a Structure Based IUPAC Identifier for 3-D Structures of AIDS Inhibitors



M D. Prasanna, H Rodriguez, J Vondrasek, A Wlodawer, Talapady N. Bhat


The human immunodeficiency virus encodes an aspartic protease which is responsible for posttranslational proteolytic processing of the gag and gag-pol polyprotein gene products into mature functional proteins. Following these proteolytic activities, the viral particle undergoes a morphological transformation from non-infectious to infectious virions. Despite the widespread availability of drugs for blocking this proteolytic activity, treatment of AIDS is still a work in progress. Drugs that belong to the class of protease inhibitors bind to the active site of HIV protease. In general the active site is considered to be fairly rigid and the inhibitor fills this cavity by exhibiting chemical and geometrical complementarity to the amino-acid residues of the protein. Different drugs predominantly differ in the way they organize themselves inside the active site of the enzyme, as revealed by X-ray three-dimensional structure of the enzyme/drug complex. For this reason, X-ray crystallographic data play a major role in rational design of AIDS drugs. Efficient and accurate indexing of inhibitor compounds and their components that target specific pockets of the enzyme is crucial for rapid and reliable inhibitor structure comparison and drug design studies. The work presented in this study describes the application of a developmental version of a new IUPAC standard to index inhibitors and we illustrate its use in a web resource for AIDS inhibitors ( The index, called IUPAC-International Chemical Identifier (InChI), is generated in several steps using the 3-D structure data for an inhibitor. The HIV Structural Reference Database (HIVSDB) website has received over 1.3 million hits during the last seven months.
Journal of Bioinformatics and Computational Biology


2-D structures, 3-D structures, enzyme drug interaction, HIV structures, INChI, indexing of chemical compounds, PDB HET groups


Prasanna, M. , Rodriguez, H. , Vondrasek, J. , Wlodawer, A. and Bhat, T. (2008), InChI a Structure Based IUPAC Identifier for 3-D Structures of AIDS Inhibitors, Journal of Bioinformatics and Computational Biology (Accessed June 18, 2024)


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Created October 16, 2008