About: RMSD of each of the three ligands (compared to the initial solvated, minimized and equilibrated bound coordinates) during 200 nanoseconds of molecular dynamics simulation. From top to bottom: (A) benzamidine (in trypsin), (B) oseltamivir (in neuraminidase), and (C) amprenavir in HIV-1 protease.

1HPV, 1S0R, 2QWK

Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking 3

Information

Details.

Scientist
Helen M. Deeks, Rebecca K. Walters, Stephanie R. Hare, Michael B. O’Connor, Adrian J. Mulholland, and David R. Glowacki
Protein
HIV-1 protease, trypsin, neuraminidase
Ligand
Amprenavir, Benzamidine, Oseltamivir
Simulation Duration
not available
InChIKey
YMARZQAQMVYCKC-OEMFJLHTSA-N
SMILES
CC(C)CN(C[C@H]([C@H](CC1=CC=CC=C1)NC(=O)O[C@H]2CCOC2)O)S(=O)(=O)C3=CC=C(C=C3)N
Molecular Formula
C25H35N3O6S
Protein Details
HIV-1 protease is a retroviral aspartyl protease, an enzyme involved with peptide bond hydrolysis in retroviruses, that is essential for the life-cycle of HIV, the retrovirus that causes AIDS. Trypsin A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. neuraminidase is an exosialidase (EC 3.2.1.18) which cleaves α-ketosidic linkage between the sialic (N-acetylneuraminic) acid and an adjacent sugar residue
Ligand Details
"Amprenavir is a synthetic derivative of hydroxyethylamine sulfonamide that selectively binds to and inhibits human immunodeficiency virus (HIV) protease.Benzamidine is a carboxamidine that is benzene carrying an amidino group. It has a role as a serine protease inhibitor. It is a member of benzenes and a carboxamidine. It derives from a benzoic acid. It is a conjugate base of a benzamidine(1+) Oseltamivir (marketed as the product TamifluⓇ), is an antiviral neuraminidase inhibitor used for the treatment and prophylaxis of infection with influenza viruses A (including pandemic H1N1) and B."
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