Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study
Abstract
:1. Introduction
2. Results and Discussion
2.1. Structural Features of SpFADS
2.2. Conformational Changes in the RFK Domain
2.3. Surface Properties of SpFADS
2.4. Oxidized and Reduced RF-Binding Modes in the RFK Domain
2.5. FMN-Binding Mode in the FMNAT Domain
2.6. Pharmacophore Model
3. Materials and Methods
3.1. Protein and Substrate Preparation
3.2. Molecular Docking Simulation
3.3. 3D-Pharmacophore Modeling
3.4. Structure Visualization
4. Conclusions and Future Perspectives
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Rank | Binding Energy (kcal/mol) (Oxidized Form) | Binding Energy (kcal/mol) (Reduced Form) |
---|---|---|
1 | −9.0 | −9.4 |
2 | −9.0 | −9.2 |
3 | −9.0 | −9.1 |
4 | −8.9 | −8.9 |
5 | −8.8 | −8.8 |
6 | −8.6 | −8.7 |
7 | −8.6 | −8.2 |
8 | −7.8 | −7.3 |
9 | −7.4 | −7.3 |
10 | −7.1 | −7.2 |
Rank | Conformer | Binding Energy (kcal/mol) (with ATP) | Binding Energy (kcal/mol) (without ATP) |
---|---|---|---|
1 | C1 | −9.1 | −8.9 |
2 | C2 | −9.1 | −8.8 |
3 | C3 | −9.0 | −8.8 |
4 | C4 | −8.8 | −8.7 |
5 | C5 | −8.8 | −8.6 |
6 | C6 | −8.7 | −8.5 |
7 | C7 | −8.6 | −8.1 |
8 | C8 | −8.4 | −8.1 |
9 | C9 | −8.3 | −8.1 |
10 | C10 | −8.1 | −8.1 |
Compound | Chemical Structure |
---|---|
1 | |
2 | |
3 | |
4 | |
5 | |
6 | |
7 | |
8 | |
9 |
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Kwon, S. Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study. Int. J. Mol. Sci. 2023, 24, 3121. https://doi.org/10.3390/ijms24043121
Kwon S. Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study. International Journal of Molecular Sciences. 2023; 24(4):3121. https://doi.org/10.3390/ijms24043121
Chicago/Turabian StyleKwon, Sunghark. 2023. "Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study" International Journal of Molecular Sciences 24, no. 4: 3121. https://doi.org/10.3390/ijms24043121