Molecular dynamics data for compound and Mycobacterium tuberculosis shikimic acid kinase targets

Published: 27 September 2023| Version 2 | DOI: 10.17632/725kx83gts.2
Hinata Taniguchi, Shuhei Kawamoto, kohei monobe,


This repository contains data on the molecular dynamics (MD) of Mycobacterium tuberculosis shikimic acid kinase (MtSK) and (2-[(5Z)-5-(1-benzyl-5-bromo-2oxoindol-3-ylidene)-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]acetic acid). MtSK crystal structure was obtained from the Protein Data Bank (PDB ID: 2IYQ). The simulation system was created using Solution Builder on a CHARMM-GUI server with the compound conformation output from GOLD. The system was solvated using the TIP3P water model, and the necessary ions were added to balance the charges. The energies were minimized in up to 5,000 steps using the steepest descent method. Equilibration was performed for 100 ps under the standard NVT and NPT conditions. The temperature and pressure were adjusted to 310 K and 1 bar, respectively. The final MD simulation was performed for 100 ns with a 2 fs time step of under the NPT conditions. Gromacs 2021.4 was used for the simulations. Various analyses, ranging from energy calculations to Sasa analysis, were performed on the obtained trajectories.



Kyushu Kogyo Daigaku


Molecular Mechanics with Molecular Dynamics