Molecular Docking Analysis of ABL Kinase-Imatinib Complex

Crystal structure of the ABL kinase in complex with imatinib was obtained from Protein Data Bank (PDB: 1IEP); PT5 was built by ChemDraw Professional 16. Before the docking simulations, PT5 and 1IEP preparation included the addition of hydrogens, the assignment of bond order, and assessment of the correct protonation as previously described [46 (link),47 (link)]. The MOE 2019.01 software (Chemical Computing Group, Montreal, Canada) was employed for the preparation, interactive docking, visualization and the analysis procedures using its default parameters [48 (link),49 (link),50 (link)].

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I. Ciftci H., O. Radwan M., E. Ozturk S., Ulusoy N.G., Sozer E., E. Ellakwa D., Ocak Z., Can M., F.S. Ali T., I. Abd-Alla H., Yayli N., Tateishi H., Otsuka M, & Fujita M. (2019). Design, Synthesis and Biological Evaluation of Pentacyclic Triterpene Derivatives: Optimization of Anti-ABL Kinase Activity. Molecules, 24(19), 3535.

Publication 2019

ChemDraw Professional 16 MOE 2019.01 software

Hydrogens Imatinib Kinase

Corresponding Organization : Kumamoto University

Other organizations : National Research Centre, Ege University, Al-Azhar University, Kocaeli Üniversitesi, Izmir Kâtip Çelebi University, Minia University, Karadeniz Technical University

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Variable analysis

dependent variables

Docking simulations

control variables

Crystal structure of the ABL kinase in complex with imatinib obtained from Protein Data Bank (PDB: 1IEP)
Preparation of PT5 and 1IEP including the addition of hydrogens, assignment of bond order, and assessment of the correct protonation
Use of MOE 2019.01 software with default parameters for preparation, interactive docking, visualization and analysis procedures

controls

Positive control: Not specified
Negative control: Not specified

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