Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 663
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
Target unique ID: 6032
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_547 LGA11 Molecule Kanamycin 52.8 nM PBS with 10% (v/v) methanol 22793869
Structure information of aptamer
Aptamer Sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
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_547 Description LGA11
Aptamer chemistry RNA Length 79 nt
GC content 57.0% Molecular weight 25,496.16 Da
Molarity of 1 μg/μl solution 39.22 μM Number of G-quadruplexes 2
G-Score 19 Function Aptasensor
Sequence GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
Applications Detection of antibiotics
Target information
Type Detail Type Detail
PubChem ID 6032 Molecular name Kanamycin
Molecular formula C18H36N4O11 Molecular weight 484.5
IUPAC name (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol InChIKey SBUJHOSQTJFQJX-NOAMYHISSA-N
LogP -7.291 Topological polar surface area 282.61
Hydrogen bond acceptor 15 Hydrogen bond donor 11

Synonym(s):
kanamycin; KANAMYCIN A; 59-01-8; Kanamycin Base; Kanamycin sulfate; Kanamycine; KanamycinA; UNII-EQK9Q303C5; CHEBI:17630; 8063-07-8; 4,6-Diamino-2-hydroxy-1,3-cyclohexane 3,6'diamino-3,6'-dideoxydi-alpha-D-glucoside; EQK9Q303C5; KAN; (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol; Kanamycinum; Kanamicina; C18H36N4O11; 2-(aminomethyl)-6-[4,6-diamino-3-[4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol; Kanamicina [Italian]; KM (the Antibiotic); Kanamycin [INN:BAN]; Kanamycine [INN-French]; Kanamycinum [INN-Latin]; 4,6-diamino-2-hydroxy-1,3-cyclohexylene 3,6'-diamino-3,6'-dideoxydi-D-glucopyranoside; (1S,2R,3R,4S,6R)-4,6-diamino-3-[(6-amino-6-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside; HSDB 3107; EINECS 200-411-7; BRN 0061647; Kanamycin,(S); Liposomal Kanamycin; (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]tetrahydropyran-3,4,5-triol; Amikacin EP Impurity D; Prestwick3_000394; Kantrex (1:1 sulfate); Klebcil (1:1 sulfate); SCHEMBL2735; CHEMBL1384; Glucopyranoside, 4,6-diamino-2-hydroxy-1,3-cyclohexylene 3,6'-diamino-3,6'-dideoxydi-, D-; BSPBio_000607; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1,4))-2-deoxy-; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1-6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1-4))-2-deoxy-; DivK1c_000024; BPBio1_000669; DTXSID3023184; KBio1_000024; NINDS_000024; ZINC8214590; BDBM50031282; AKOS025293505; DB01172; IDI1_000024; SMP2_000007; NCGC00179506-01; NCGC00179506-05; AS-14003; K434; AB00513827; C01822; K-0250; BRD-K08327065-065-01-9; Q27094615; Kanamycin sulfate, Antibiotic for Culture Media Use Only; UNII-RUC37XUP2P component SBUJHOSQTJFQJX-NOAMYHISSA-N; (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy-alpha-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside; (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-((1R,2R,3S,4R,6S)-4,6-diamino-3-((2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)-2-hydroxycyclohexyloxy)tetrahydro-2H-pyran-3,4,5-triol; (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-3-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}oxane-3,4,5-triol; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->4))-2-deoxy-; D-Streptamine, O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1.fwdarw.6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1.fwdarw.4))-2-deoxy-; Kanamycin solution from Streptomyces kanamyceticus, 10 mg/mL in 0.9% NaCl, sterile-filtered, BioReagent, suitable for cell culture; Kanamycin solution from Streptomyces kanamyceticus, 50 mg/mL in 0.9% NaCl, BioReagent, liquid, sterile-filtered, suitable for cell culture; O-3-Amino-3-deoxy-.alpha.-D-glucopyranosyl-(1->6)-O-[6-amino-6-deoxy-.alpha.-D-glucopyranosyl-(1->4)]-2-deoxy-D-streptamine; O-3-amino-3-deoxy-alpha-D-glucopyranosyl-(1->6)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->4))-2-deoxy-D-streptamine

Activity data
Interaction ID 580
Target type Molecule
Target unique ID 3081545
Activity 28.4 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 651
Target type Molecule
Target unique ID 3467
Activity 22.3 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 663
Target type Molecule
Target unique ID 6032
Activity 52.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 723
Target type Molecule
Target unique ID 8378
Activity 40.3 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869

No relevant experimental diagram

 Interaction ID 757
Target type Molecule
Target unique ID 165580
Activity 21.4 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 779
Target type Molecule
Target unique ID 19649
Activity 49.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Interaction ID 797
Target type Molecule
Target unique ID 36294
Activity 19.2 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

GNP-aptamer sensor detection of aminoglycosides
PubMed ID 22793869
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_548 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC 73.42%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 53.33%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 53.16%
Apta_1224 RNA GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC 53.00%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_1221 RNA GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC 52.00%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 51.90%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 51.72%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 51.38%
Apta_398 RNA GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 51.14%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 51.11%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 51.09%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 51.06%
Apta_38 RNA GGUAGAUACGAUGGAUACCCCCUGUGGCCCGUCAACACAGGGGAAGUGGCAUGACGCGCAGCCA 50.63%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 50.63%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 50.63%
Apta_400 RNA GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA 50.63%
Apta_594 RNA GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC 50.63%
Apta_276 RNA GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC 50.59%

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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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