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PTP1B aptamer
Description
In 2010, Brent Townshend et al. used the SELEX method to isolate the aptamer with high compatibility for the protein tyrosine phosphatase 1B (PTP1B). The C13 RNA aptamer identified in this work by using the SELEX procedure not only binds tightly to PTP1B, but also inhibits its phosphatase activity[1].SELEX
In 2010, Brent Townshend et al. create an RNA aptamer targeted to protein tyrosine phosphatase 1B (PTP1B) by SELEX[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw.5'-GGGAAUGGAUCCACAUCUACUGUGAUCAAUUUGGCAAUCCGCCACACGAGACUGCAGACUUGACGAAGCUU-3'
Ligand information
SELEX ligand
Tyrosine-protein phosphatase non-receptor type 1 also known as protein-tyrosine phosphatase 1B (PTP1B) is an enzyme that is the founding member of the protein tyrosine phosphatase (PTP) family. In humans it is encoded by the PTPN1 gene. PTP1B is a negative regulator of the insulin signaling pathway and is considered a promising potential therapeutic target, in particular for treatment of type 2 diabetes. It has also been implicated in the development of breast cancer and has been explored as a potential therapeutic target in that avenue as well.-----From Wiki
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Protein tyrosine phosphatase 1B (PTP1B) | P18031 | IPR012265 | 49.97 kDa | MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY | 1Q1M | 5770 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| C13 | 5'-GGGAAUGGAUCCACAUCUACUGUGAUCAAUUUGGCAAUCCGCCACACGAGACUGCAGACUUGACGAAGCUU-3' | Protein tyrosine phosphatase 1B (PTP1B) | 200 pM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 1XBO-A | 52.4 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 1SUG-A | 52.4 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 6B90-A | 52.2 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 3I80-A | 52.1 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 6OLQ-A | 52.0 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 2CM8-A | 51.9 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 6PG0-A | 51.9 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 6PHS-A | 51.8 | 0.2 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 7S4F-A | 51.8 | 0.3 | Protein-tyrosine phosphatase, non-receptor type 1 |
| 1PTY-A | 51.7 | 0.3 | Protein tyrosine phosphatase 1b |
References
[1] An RNA aptamer that selectively inhibits the enzymatic activity of protein tyrosine phosphatase 1B in vitro.Townshend, B., Aubry, I., Marcellus, R. C., Gehring, K., & Tremblay, M. L.
Chembiochem : a European journal of chemical biology, 11(11), 1583–1593. (2010)