Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 223
Aptamer sequence: AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA
Target unique ID: P04626
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_219 | HB5 | Protein | ERBB2_HUMAN | 18.9 nM | Hanks buffer with 0.1 mg/mL salmon sperm DNA and 1 mg/mL of BSA | 22817844 |
Structure information of aptamer
| Aptamer Sequence: | AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA |
| The optimal secondary structure in dot-bracket notation: | ....................(((((.....((((.....((........)).....)))).....)))))................ |
| The centroid secondary structure in dot-bracket notation: | ...................................................................................... |
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_219 | Description | HB5 |
| Aptamer chemistry | DNA | Length | 86 nt |
| GC content | 43.0% | Molecular weight | 26,510.80 Da |
| Molarity of 1 μg/μl solution | 37.72 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | AACCGCCCAAATCCCTAAGAGTCTGCACTTGTCATTTTGTATATGTATTTGGTTTTTGGCTCTCACAGACACACTACACACGCACA | ||
| Applications | Targeting ligand for delivering doxorubicin (Dox) to breast cancer cells in vitro | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P04626 | Protein name | Receptor tyrosine-protein kinase erbB-2 (EC 2.7.10.1) (Metastatic lymph node gene 19 protein) (MLN 19) (Proto-oncogene Neu) (Proto-oncogene c-ErbB-2) (Tyrosine kinase-type cell surface receptor HER2) (p185erbB2) (CD antigen CD340) |
| Gene name(s) | ERBB2 HER2 MLN19 NEU NGL | Organism | Receptor tyrosine-protein kinase erbB-2 (EC 2.7.10.1) (Metastatic lymph node gene 19 protein) (MLN 19) (Proto-oncogene Neu) (Proto-oncogene c-ErbB-2) (Tyrosine kinase-type cell surface receptor HER2) (p185erbB2) (CD antigen CD340) |
| Status | reviewed in uniprot database | Length | 1255 |
| Mass | 137,910 | Activity regulation | Activated by dimerization |
| Involvement in disease | Glioma (GLM) | Catalytic activity | Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein] |
| PDB ID(s) | 1MFG;1MFL;1MW4;1N8Z;1QR1;1S78;2A91;2JWA;2KS1;2L4K;2N2A;3BE1;3H3B;3MZW;3N85;3PP0;3RCD;3WLW;3WSQ;4GFU;4HRL;4HRM;4HRN;4NND;5K33;5KWG;5MY6;5O4G;5OB4;5TQS;6ATT;6BGT;6J71;6LBX;6OGE;7JXH;7MN5;7MN6;7MN8; |
 |
Function | Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. |
Activity data
 |
Interaction ID | 223 |
| Target type | Protein | |
| Target unique ID | P04626 | |
| Activity | 18.9 nM | |
| Binding Conditions/Buffer | Hanks buffer with 0.1 mg/mL salmon sperm DNA and 1 mg/mL of BSA |
|
| Assay | Quantitative assay of HB5’s binding affinity |
|
| PubMed ID | 22817844 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_321 | DNA | AACCGCCCAAATCCCTAAGAGTCGGACTGCAACCTATGCTATCGTTGATGTCTGTCCAAGCAACACAGACACACTACACACGCACA | |
| Apta_316 | DNA | CCGCCCAAATCCCTAAGAGAAGACTGTAATGACATCAAACCAGACACACTACACACGCA | |
| Apta_1113 | DNA | CCGCCCAAATCCCTAAGAGCACAAACACCAAACACAACCACCCCAACCAGACACACTACACACGCA | |
| Apta_805 | DNA | ATACCAGCTTATTCAATTAGGCGGTGCATTGTGGTTGGTAGTATACATGAGGTTTGGTTGAGACTAGTCGCAAGATATAGATAGTAAGTGCAATCT | |
| Apta_726 | DNA | TACCAGTGCGATGCTCAGGCCGATGTCAACTTTTTCTAACTCACTGGTTTTGCCTGACGCATTCGGTTGAC | |
| Apta_990 | DNA | AACCCAACCCCGCACCATTAGTCTAAATTTTCGCGACGGAACACAGCAACAACTCCCCA | |
| Apta_174 | DNA | AGCAGCACAGAGGTCAGATGTCGGTCTTGTGTATACATACCCGTGTGTTTTCATCTCAGGCCTATGCGTGCTACCGTGAA | |
| Apta_810 | DNA | ACAGCATCCCCATGTGAACAATCGCATTGTGATTGTTACGGTTTCCGCCTCATGGACGTGCTG | |
| Apta_228 | DNA | AGCAGCACAGAGGTCAGATGCGGCGCGGGGTCTTTTACAAATAGTTGTCCTAGCCACGCCTATGCGTGCTACCGTGAA | |
| Apta_233 | DNA | AGCAGCACAGAGGTCAGATGTGAAACATAGCATATTTACTTATGTCGCCTTGCCGGTTCCTATGCGTGCTACCGTGAA | |
| Apta_786 | DNA | ATCCAGAGTGACGCAGCATTTGTATCCTATTTTGTTTATGTAATTGTCGTTGATCATGTGGACACGGTGGCTTAGT | |
| Apta_173 | DNA | AGCAGCACAGAGGTCAGATGGCAGGTTTCGACGTACAATGCTATGGAGGCTTTATGATCGCCTATGCGTGCTACCGTGAA | |
| Apta_175 | DNA | AGCAGCACAGAGGTCAGATGAGGACTGTCGATAAGTATAATGGCAAGTAGCTCGATACATCCTATGCGTGCTACCGTGAA | |
| Apta_451 | DNA | ATACCAGCTTATTCAATTGAGTAAGAGTGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCAATCT | |
| Apta_452 | DNA | ATACCAGCTTATTCAATTGAAGAGTATAAAAAGAGTGATTATCTTTTGTAGGTTTTTTAGATAGTAAGTGCAATCT | |
| Apta_531 | DNA | ATACGGGAGCCAACACCACATCGACTTACGAATCAACGCGTTTATTATTGGTTCAGAGCAGGTGTGACGGAT | |
| Apta_587 | DNA | GGAATGGATCCACATCCATGGATGGGCAATGCGGGGTGGAGAATGGTTGCCGCACTTCGGCTTCACTGCAGACTTGACGAAGCTT | |
| Apta_826 | DNA | ATCCGTCACACCTGCTCTGCACGGGCTCAGTTTGGCTTTGTATCCTAAGAGGGATGGTGTTGGCTCCCGTAT | |
| Apta_836 | DNA | TGAGCCCAAGCCCTGGTATGTTACAGTATGCTACCTCTACTTGAAGGTTGGTCGACGCGGGGCAGGTCTACTTTGGGATC | |
| Apta_842 | DNA | TGAGCCCAAGCCCTGGTATGTGTGGGGTCCTGGATTATGTTTAGCGTCTTTCGCAGTGGGGGCAGGTCTACTTTGGGATC |
DEV TOOL
 |
 |
 |
 |