Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway
Abstract
:1. Introduction
2. Results and Discussion
2.1. CDOCKER Energy, CDOCKER Interaction Energy and the Binding Energy
2.2. Binding Pocket Analysis
2.2.1. Binding Pocket of the TNFα
2.2.2. Nuclear Factor κB Complex (NF-κB) Complex
2.2.3. Inhibitor of ΚB Kinase Complex (IKKs)
IKKβ
IKKα (human) with Zerumbone
3. Experimental Section
3.1. Protein and Ligand Starting Structures
Pathways | Molecule (PDB ID) |
---|---|
Tumour necrosis factor | Tumor necrosis factor (2AZ5) |
IKKβ (3RZF) | |
IKKα (Predicted) | |
Nuclear factor κβ (p50) (1SVC) | |
Nuclear factor κβ RelA (p65) (2RAM) |
3.2. Homology Modeling
3.3. Preparation of Structures for Docking
3.4. Docking with CDOCKER
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Fatima, A.; Abdul, A.B.H.; Abdullah, R.; Karjiban, R.A.; Lee, V.S. Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway. Int. J. Mol. Sci. 2015, 16, 2747-2766. https://doi.org/10.3390/ijms16022747
Fatima A, Abdul ABH, Abdullah R, Karjiban RA, Lee VS. Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway. International Journal of Molecular Sciences. 2015; 16(2):2747-2766. https://doi.org/10.3390/ijms16022747
Chicago/Turabian StyleFatima, Ayesha, Ahmad Bustamam Hj. Abdul, Rasedee Abdullah, Roghayeh Abedi Karjiban, and Vannajan Sanghiran Lee. 2015. "Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway" International Journal of Molecular Sciences 16, no. 2: 2747-2766. https://doi.org/10.3390/ijms16022747