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Analysis of structural water and CH···π interactions in HIV1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT

Analysis of structural water and CH···π interactions in HIV1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT,10.1007/s00

Analysis of structural water and CH···π interactions in HIV1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT   (Citations: 1)
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A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously–the structural water–is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L. Figure Concurrent two CH···π interactions of an aromatic ring in the HIV-protease system 1D4L, located using HBPredicT
Journal: Journal of Molecular Modeling - J MOL MODEL , vol. 17, no. 2, pp. 401-413, 2011
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    • ...1 and 2 ,t here are some water molecules that interact with the inhibitor stabilizing the complex (Fig. 3a and b). These five water molecules contributed in stabilizing the EH58 inhibitor interaction at the active site of the protein through hydrogen bond-type ligand-water [55] in values 2.18 Å in O48 atom, 1.98 Å in O49 atom, 1.92 Å in O41 atom, 2.04 Å in O39 atom and 2.08 in O32 atom for A model (Fig. 1b, e and f). In ...
    • ... contributed in stabilizing the EH58 inhibitor interaction at the active site of the protein through hydrogen bond-type ligand-water [55] in values 2.18 Å in O48 atom, 1.98 Å in O49 atom, 1.92 Å in O41 atom, 2.04 Å in O39 atom and 2.08 in O32 atom for A model (Fig. 1b, e and f). In B model, three water molecules contributed in stabilizing the ligand interaction at the active site of the protein through hydrogen bond-type ...

    Natália de Farias Silvaet al. Computational analysis of aspartic protease plasmepsin II complexed wi...

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