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PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K - Nucleic Acids Res. (2014)

Bottom Line: This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery.Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM.Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.

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Captured image from the superimposition viewer, which shows the superimposition of an STI-binding pocket of 1IEP to a putative pocket of 2GK9. The query ligand and its pocket are shown in red and pink, and the target pocket is shown in cyan.
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Figure 5: Captured image from the superimposition viewer, which shows the superimposition of an STI-binding pocket of 1IEP to a putative pocket of 2GK9. The query ligand and its pocket are shown in red and pink, and the target pocket is shown in cyan.

Mentions: We present an example here: similarity between the imatinib (HET: STI)-binding pocket of the tyrosine protein kinase ABL (PDB ID: 1IEP) (23) and a putative pocket of phosphatidylinositol-4-phosphate 5 (P4P5)-kinase (PDB ID: 2GK9). Despite adopting different folds (with CATH codes ‘1.10.510.10, 3.30.200.20’ and ‘3.30.800.10’, respectively) (Figure 5 and Supplementary Figure S3), 25 residues of the two pockets are aligned with an Root-Mean-Square Deviation (RMSD) of 2.77 Å, suggesting that imatinib would bind to P4P5-kinase, which is consistent with its known Kd value of 380 nM (24).


PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K - Nucleic Acids Res. (2014)

Captured image from the superimposition viewer, which shows the superimposition of an STI-binding pocket of 1IEP to a putative pocket of 2GK9. The query ligand and its pocket are shown in red and pink, and the target pocket is shown in cyan.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383952&req=5

Figure 5: Captured image from the superimposition viewer, which shows the superimposition of an STI-binding pocket of 1IEP to a putative pocket of 2GK9. The query ligand and its pocket are shown in red and pink, and the target pocket is shown in cyan.
Mentions: We present an example here: similarity between the imatinib (HET: STI)-binding pocket of the tyrosine protein kinase ABL (PDB ID: 1IEP) (23) and a putative pocket of phosphatidylinositol-4-phosphate 5 (P4P5)-kinase (PDB ID: 2GK9). Despite adopting different folds (with CATH codes ‘1.10.510.10, 3.30.200.20’ and ‘3.30.800.10’, respectively) (Figure 5 and Supplementary Figure S3), 25 residues of the two pockets are aligned with an Root-Mean-Square Deviation (RMSD) of 2.77 Å, suggesting that imatinib would bind to P4P5-kinase, which is consistent with its known Kd value of 380 nM (24).

Bottom Line: This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery.Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM.Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan k-tomii@aist.go.jp.

Show MeSH
Related in: MedlinePlus