Перегляд класифікації конформацій активного центру протеїнтирозинфосфатази 1B
Our previous work on the classification of binding site conformations of protein tyrosine phosphatase 1B was published in 2012. It was then found that 102 active sites from 91 PDB files can be divided into 5 major clusters. Since that time, the number of the enzyme PDB files, which are deposited in...
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| Date: | 2024 |
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| Main Authors: | , , |
| Format: | Article |
| Language: | English |
| Published: |
V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine
2024
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| Subjects: | |
| Online Access: | https://bioorganica.com.ua/index.php/journal/article/view/84 |
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| Journal Title: | Ukrainica Bioorganica Acta |
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Ukrainica Bioorganica Acta| Summary: | Our previous work on the classification of binding site conformations of protein tyrosine phosphatase 1B was published in 2012. It was then found that 102 active sites from 91 PDB files can be divided into 5 major clusters. Since that time, the number of the enzyme PDB files, which are deposited in the RCSB Protein Data Bank, and the number of PTP1B crystal structures in these files have been quadrupled emphasizing the importance of this enzyme as a target for drug design. In the present paper, 793 binding sites from 374 PDB files of PTP1B available now were analyzed. Although the clustering results seem to have remained the same since the first investigation, some centroids have been changed and the number of structures in the clusters has increased. Clusters with closed WPD loops, except one, retained their centroids. Most new conformations with open WPD-loop appear in one cluster, which includes crystal structures where ligands occupy the catalytic pockets or are located at the enzyme allosteric sites. The updated clusters can be used for molecular docking-based designing inhibitors of PTP1B |
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