Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 358
Aptamer sequence: GAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCC
Target unique ID: P21860
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_353 A30 Protein ERBB3_HUMAN 45 nM 10 mM HEPES (pH 7.4), 100 mM NaCl, and 2.5 mM MgCl2 12874383
Structure information of aptamer
Aptamer Sequence: GAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCC
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_353 Description A30
Aptamer chemistry RNA Length 79 nt
GC content 59.5% Molecular weight 24,670.52 Da
Molarity of 1 μg/μl solution 40.53 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence GAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCC
Applications Inhibits hrg-dependent tyrosine phosphorylation of HER2 and the hrg-induced growth response of MCF7 cells
Target information
Type Detail Type Detail
Uniprot ID P21860 Protein name Receptor tyrosine-protein kinase erbB-3 (EC 2.7.10.1) (Proto-oncogene-like protein c-ErbB-3) (Tyrosine kinase-type cell surface receptor HER3)
Gene name(s) ERBB3 HER3 Organism Receptor tyrosine-protein kinase erbB-3 (EC 2.7.10.1) (Proto-oncogene-like protein c-ErbB-3) (Tyrosine kinase-type cell surface receptor HER3)
Status reviewed in uniprot database Length 1342
Mass 148,098 Activity regulation N/A
Involvement in disease Lethal congenital contracture syndrome 2 (LCCS2) Catalytic activity Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]
PDB ID(s)
1M6B;2L9U;3KEX;3LMG;3P11;4LEO;4P59;4RIW;4RIX;4RIY;5CUS;5O4O;5O7P;6KBI;6OP9;7BHE;7BHF;7D85;7MN5;7MN6;7MN8;
Function Tyrosine-protein kinase that plays an essential role as cell surface receptor for neuregulins.
Activity data
Interaction ID 358
Target type Protein
Target unique ID P21860
Activity 45 nM
Binding Conditions/Buffer

10 mM HEPES (pH 7.4), 100 mM NaCl, and 2.5 mM MgCl2
Assay

Binding of A30 to HER3ECD and cellular HER3
PubMed ID 12874383
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_601 RNA GGGAAUUCCGCGUGUGCGCCGCGGAAGAGGGAAUAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCCC 58.23%
Apta_598 RNA GGGAAUUCCGCGUGUGCGCCGCGGAAGACGUUGGAAGGAUAGAUACCUACAACGGGGAAUAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCCC 55.91%
Apta_696 RNA GAGUGCGCCCAUUGAUAAGAGCGUAGGUUCAACGGAGUCGUAGUCGUUCUCAAGUUGACGGUGCAUUAGAGUCCU 55.70%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 55.32%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 53.33%
Apta_499 RNA GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC 53.09%
Apta_549 RNA GGAGCUCAGCCUUCACUGCAUGAUAAACCGAUGCUGGGCGAUUCUCCUGAAGUAGGGGAAGAGUUGUCAUGUAUGGGGGCACCACGGUCGGAUCCUG 52.58%
Apta_413 RNA GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU 52.53%
Apta_874 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC 52.14%
Apta_563 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGAAAGCCAAAGCCGUAGCGCAGAUGAUCUCGCCAUCAGUACCGAAACGGUAGCGAGAGCUC 52.04%
Apta_416 RNA GGACCUCGGCGAAAGCCGGUAACGCCACAAGUCGGAGGGUAAGAUCUGACAGGAACUGGGUGACGGAGGUUAGGUGC 51.90%
Apta_431 RNA CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGUUC 51.90%
Apta_645 RNA CUGGACGACGGGGACGCCACUGGACUAGGUAAGCCAGGACCGUACGUCGGGAGCCGUCAGAAUA 51.90%
Apta_59 RNA GGACCUCGGCGAAAGCUAACGUCUCAUGGCUAAAUUGCCAUGUUGCUACAAAUGAUAUGACUAGAGAGGUUAGGUGCCUCGUGAUGUCCAGUCGC 51.58%
Apta_936 RNA GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC 51.52%
Apta_1222 RNA GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC 51.00%
Apta_557 RNA GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG 50.91%
Apta_156 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU 50.63%
Apta_297 RNA AUACCAGCUUAUUCAAUUGCCUGAGUAGCUGGGUCCGUCCCCACACAUUACCAUUUGUAGAUAGUAAGUGCAAUCU 50.63%
Apta_575 RNA AGAGCUUGACGGUCCCGAGAGUCGAGCCCAAGCUGACACUGGACCUUUGCGGACCACGUGUUGAUCGUCG 50.63%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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