Literature summary for 3.4.23.16 extracted from

Cong, Y.; Li, Y.; Jin, K.; Zhong, S.; Zhang, J.Z.H.; Li, H.; Duan, L.
Exploring the reasons for decrease in binding affinity of HIV-2 against HIV-1 protease complex using interaction entropy under polarized force field (2018), Front. Chem., 6, 380 .

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Inhibitors

Inhibitors	Comment	Organism	Structure
amprenavir	-	Human immunodeficiency virus 1
darunavir	-	Human immunodeficiency virus 1
additional information	analysis of the differences of binding patterns between the two type HIV proteases, HIV-1 protease and HIV-2 protease, using the interaction entropy (IE) method for the entropy change calculation combined with the polarized force field, and the two inhibitors darunavir and amprenavir. The bridging water W301 is favorable to the binding of HIV-1 complexes, in contrast to HIV-2 protease complexes. The volume of pocket, B-factor of Calpha atoms and the distance of flap tip in HIV-2 complexes are smaller than that of HIV-1 consistently. Predicated hot-spot residues (Ala28/Ala28', Ile50/Ile50', and Ile84/Ile84') are nearly same in the four systems. The contribution to the free energy of Asp30 residue is more favorable in HIV-1 system than in HIV-2 system. Molecular dynamics simulation and binding free energy calculations, and protonation states of the enzymes, overview	Human immunodeficiency virus 1

Organism

Organism	UniProt	Comment	Textmining
Human immunodeficiency virus 1	P04587	Gag-Pol polyprotein; HIV-1 BH5 isolate	-

Synonyms

Synonyms	Comment	Organism
HIV-1 protease	-	Human immunodeficiency virus 1
PR1	-	Human immunodeficiency virus 1

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Release 2023.1 (January 2023)