Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 796
Aptamer sequence: GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA
Target unique ID: 36294
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_720 J6(13) Molecule Tobramycin 2 nM 140 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1mM MgCl2, and 20 mM Tris Acetate (pH 7.4) 9383430
Structure information of aptamer
Aptamer Sequence: GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA
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_720 Description J6(13)
Aptamer chemistry RNA Length 109 nt
GC content 51.4% Molecular weight 35,048.70 Da
Molarity of 1 μg/μl solution 28.53 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA
Applications Detection of the aminoglycoside antibiotic tobramycin
Target information
Type Detail Type Detail
PubChem ID 36294 Molecular name Tobramycin
Molecular formula C18H37N5O9 Molecular weight 467.5
IUPAC name (2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol InChIKey NLVFBUXFDBBNBW-PBSUHMDJSA-N
LogP -6.296 Topological polar surface area 268.17
Hydrogen bond acceptor 14 Hydrogen bond donor 10

Synonym(s):
tobramycin; 32986-56-4; Nebramycin 6; Nebramycin factor 6; 3'-Deoxykanamycin B; Tobramicin; Nebcin; Tobi; Aktob; Tobrex; Tobramycin Base; Deoxykanamycin B; Tobi Podhaler; Nebramycin VI; Bethkis; Tobradistin; NEBRAMYCIN; C18H37N5O9; Tobralex; UNII-VZ8RRZ51VK; Tobracin (TN); NSC 180514; Tobrex (TN); VZ8RRZ51VK; (2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol; Obramycin; CHEBI:28864; 1-Epitobramycin; vantobra; Tobramicina; Tobramycine; Tobramycinum; Gotabiotic; Nebicin; Tobacin; Tobrased; (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside; Kitabis Pak; Tobramycine [INN-French]; Tobramycinum [INN-Latin]; Tobramicina [INN-Spanish]; (2S,3R,4S,5S,6R)-4-amino-2-(((1S,2S,3R,4S,6R)-4,6-diamino-3-(((2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxytetrahydro-2H-pyran-2-yl)oxy)-2-hydroxycyclohexyl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,5-diol; O-3-Amino-3-deoxy-?-D-glucopyranosyl-(1-6)-O-[2,6-diamino-2,3,6-trideoxy-?-D-ribohexopyranosyl-(1-4)]-2-deoxy-D-streptamine; O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribohexopyranosyl-(1-4))-2-deoxy-D-streptamine; TOY; Nebramycin factir 6; HSDB 3259; SR-05000001726; EINECS 251-322-5; SPRC-AB01; BRN 1357507; torbamycin; Kitabis; NSC-180514; tobramycin solution for inhalation; Tobramycin,(S); Nebcin (Sulfate); NCGC00016814-01; (2S,3R,4S,5S,6R)-4-amino-2-((1S,2S,3R,4S,6R)-4,6-diamino-3-((2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxytetrahydro-2H-pyran-2-yloxy)-2-hydroxycyclohexyloxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,5-diol; Bethkis (TN); CAS-32986-56-4; MFCD00077885; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-6)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl-(1-4))-2-deoxy-; Tobramycin [2M+H]; Tobramycin [USAN:USP:INN:BAN:JAN]; Tobi (TN); Spectrum_001072; Prestwick3_000544; Spectrum2_000078; Spectrum3_000588; Spectrum4_000752; Spectrum5_001038; DSSTox_CID_3680; Tobramycin (JP17/USP); SCHEMBL2838; CHEMBL1747; DSSTox_RID_77144; DSSTox_GSID_23680; BSPBio_000587; BSPBio_002036; KBioGR_001104; KBioSS_001552; 4-(2,6-Diamino-2,3,6-trideoxy-alpha-D-glycopyranosyl)-6-(3-amino-3-deoxy-alpha-D-glycopyranosyl)-2-deoxystreptamine; MLS000069544; O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-6)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribohexopyranosyl-(1-4))-2-deoxy-D-streptamine; Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,6-tyrideoxy-alpha-D-ribohexopyranosyl-(1-6))-2-deoxy-, D-; BIDD:GT0503; SPECTRUM1500579; SPBio_000295; BPBio1_000647; DTXSID8023680; GTPL10930; KBio2_001552; KBio2_004120; KBio2_006688; KBio3_001536; AOB5629; HMS2090B16; HMS2092M17; HMS2096N09; HMS3713N09; Pharmakon1600-01500579; HY-B0441; ZINC8214692; Tox21_110626; BDBM50366778; CCG-39936; NSC757352; s2514; Tobradex (tobramycin + dexamethasone); AKOS016339662; DB00684; KS-1405; NSC-757352; NCGC00178852-01; NCGC00178852-02; (2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxy-tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]-6-(hydroxymethyl)tetrahydropyran-3,5-diol; 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL; O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl-(1-6))-2-deoxy-L-streptamine; SMR000058793; Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribohexopyranosyl-(1-6))-2-deoxy-, D-; SBI-0051915.P003; AB00513858; T2503; C00397; D00063; J10405; AB00052438-12; AB00052438_13; AB00052438_14; 986T564; SR-01000721898; Tobramycin, Antibiotic for Culture Media Use Only; Q-201837; Q1758380; SR-01000721898-2; SR-05000001726-1; SR-05000001726-2; BRD-K05619559-001-12-7; UNII-NQJ13I4Z9U component NLVFBUXFDBBNBW-PBSUHMDJSA-N; (1S,2S,3R,4S,6R)-4,6-diamino-3-(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside; (2S,3R,4S,5S,6R)-4-amino-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-6-(hydroxymethyl)oxane-3,5-diol; D-Streptamine, O-3-amino-3-deoxy-.alpha.-D-glucopyranosyl-(1->6)-O-[2,6-diamino-2,3,6-trideoxy-.alpha.-D-ribo-hexopyranosyl-(1->4)]-2-deoxy-; D-Streptamine, O-3-amino-3-deoxy-.alpha.-D-glucopyranosyl-(1->6)-O-[2,6-diamino-2,3,6-trideoxy-.alpha.-D-ribohexopyranosyl-(1->4)]-2-deoxy-; O-[3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1-->6)]-O-[2,6-diamino-2,3,6-trideoxy-alpha-D-ribohexopyranosyl-(1-->4)]-2-deoxy-D-streptamine; O-[3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1->6)]-O-[2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl-(1->4)]-2-deoxy-D-streptamine; O-3-Amino-3-deoxy-a-D-glucopyranosyl-(1-6)-O-[2,6-diamino-2,3,6-trideoxy-a -D-ribo-hexopyranosyl-(1-4)]-2-deoxy-D-streptamine

Activity data

No relevant experimental diagram

 Interaction ID 796
Target type Molecule
Target unique ID 36294
Activity 2 nM
Binding Conditions/Buffer

140 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1mM MgCl2, and 20 mM Tris Acetate (pH 7.4)
Assay

N/A
PubMed ID 9383430
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_156 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU 55.96%
Apta_1100 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU 55.96%
Apta_337 RNA GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG 55.05%
Apta_1223 RNA GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC 55.05%
Apta_695 RNA AUUGGAUCGGUAGUAUAGGUGAGACACUUCAUGCCUUUGUUGCAGGCUGGGGUGAAGGCGCUACAUGGCGUCUGAAA 54.13%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 54.13%
Apta_1226 RNA GGAGGCGCCAACUGAAUGAAGGUGUAUUUCAGUUAAAGAACUUGCUGCUUCGGCAGCGUUCUGAGUUACUAGUCCAAUAAUCCGUAACUAGUCGCGUCAC 54.13%
Apta_376 RNA GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC 53.51%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 53.21%
Apta_886 RNA GGGAGACGAUAUUCGUCCAUUCGGGUGGCCCGUGUCUGAGCGGGGACGGCCACUUGAGCGCCGCUGUCCGACUGAAUUCUCGACC 53.21%
Apta_1124 RNA GGGCGAAUUCGGGUUGGAUAGUAGGCGCAUAUGGCAUCUUCGUGGUUGUGUAUUGCCCUUUAGUGAGGGUUAAUU 53.21%
Apta_170 RNA GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC 52.29%
Apta_171 RNA GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC 52.29%
Apta_224 RNA GGGGCCACCAACGACAUUGAACCACGUAGGCUCGUUUCUGAGCCGAUCUCGAUGUUGAUAUAAAUAGUGCCCAUGGAUC 52.29%
Apta_225 RNA GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC 52.29%
Apta_415 RNA GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA 52.29%
Apta_430 RNA GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU 52.29%
Apta_548 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC 52.29%
Apta_494 RNA GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU 51.79%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 51.38%

ABOUT

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

HELP CENTER

>Contact us
>LMMD Group
>School of Pharmacy

DEV TOOL
Page last updated at 2022-05-25 10:01:57 (Asia/Shanghai) | You are visitor No. 43982
Copyright © 2019-2020 Laboratory of Molecular Modeling and Design, School of Pharmacy, East China University of Science and Technology. All rights reserved.