Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 798
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Target unique ID: 36294
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_548 LS13 Molecule Tobramycin 24.8 nM PBS with 10% (v/v) methanol 22793869
Structure information of aptamer
Aptamer Sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
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_548 Description LS13
Aptamer chemistry RNA Length 79 nt
GC content 46.8% Molecular weight 25,394.90 Da
Molarity of 1 μg/μl solution 39.38 μM Number of G-quadruplexes 2
G-Score 17 Function Aptasensor
Sequence GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Applications Detection of antibiotics
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
Interaction ID 581
Target type Molecule
Target unique ID 3081545
Activity 35.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 652
Target type Molecule
Target unique ID 3467
Activity 26.7 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 664
Target type Molecule
Target unique ID 6032
Activity 69.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 724
Target type Molecule
Target unique ID 8378
Activity 37 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 758
Target type Molecule
Target unique ID 165580
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 780
Target type Molecule
Target unique ID 19649
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 798
Target type Molecule
Target unique ID 36294
Activity 24.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_547 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC 73.42%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 59.78%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 54.43%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 52.29%
Apta_1223 RNA GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC 52.00%
Apta_576 RNA GGCACCAAAGCUGAAGUAGCGGGAUAACUCAAAUUACUUUAGGUGUAUGAAGGUGAAACUAGCAAUGAA 51.90%
Apta_410 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG 51.76%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 51.16%
Apta_1225 RNA GGAGGCGCCAACUGAAUGAAAGAGGUAACGAAAGAUGAUUGUGCCUGCUUCGGCAGUACAACUUCUCGGAUAAAUGAUUAUCCGUAACUAGUCGCGUCAC 51.00%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 50.63%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 50.63%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 50.63%
Apta_1100 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU 50.63%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 50.00%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 50.00%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 50.00%

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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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