Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 662
Aptamer sequence: GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU
Target unique ID: 6032
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_623 sla 16 Molecule Kanamycin 300 nM 500 mM NaCl, 50 mM Tris (pH 7.6) 9383431
Structure information of aptamer
Aptamer Sequence: GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU
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_623 Description sla 16
Aptamer chemistry RNA Length 80 nt
GC content 57.5% Molecular weight 25,761.32 Da
Molarity of 1 μg/μl solution 38.82 μM Number of G-quadruplexes 2
G-Score 18 Function Targeted binding
Sequence GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU
Applications Binding to aminoglycoside
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

No relevant experimental diagram

 Interaction ID 662
Target type Molecule
Target unique ID 6032
Activity 300 nM
Binding Conditions/Buffer

500 mM NaCl, 50 mM Tris (pH 7.6)
Assay

N/A
PubMed ID 9383431
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_624 RNA GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU 78.75%
Apta_719 RNA GGAAUGGAUCCACAUCUACGAAGGCUUUGAAGGUGAGACCGUGCAAAUGAGGAUGGUGUGGAUGAUUAGGGUUGUCGGUUUUCACUGCAGACUUGACGAAGCUU 63.46%
Apta_495 DNA GGGAATGGATCCACATCTACGTATTACTGCTGGTGACGAGGGCTAGACGACGTACCTTCACTGCAGACTTGACGAAGCTT 61.25%
Apta_1120 DNA GGGAATGGATCCACATCTACGAATTCGGAATGAGTGCCCTGCAAGCGAGGGCTAGCTTCACTGCAGACTTGACGAAGCTT 61.25%
Apta_587 DNA GGAATGGATCCACATCCATGGATGGGCAATGCGGGGTGGAGAATGGTTGCCGCACTTCGGCTTCACTGCAGACTTGACGAAGCTT 60.00%
Apta_1118 DNA GGGAATGGATCCACATCTACGAATTCATCAGGGCTAAAGAGTGCAGAGTTACTTAGTTCACTGCAGACTTGACGAAGCTT 60.00%
Apta_1119 DNA GGGAATGGATCCACATCTACGAATTCGGTTGTGAAGATTGGGAGCGTCGTGGCTACTTCACTGCAGACTTGACGAAGCTT 60.00%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 56.84%
Apta_909 RNA GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG 54.72%
Apta_380 RNA GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG 54.35%
Apta_1289 RNA GGGAGAGGAUACUACACGUGGAAAAACCAACAAAUUGGGAAAAAUGUUAAGGGUCCACUUCAUGCCAUUGCAUGUAGCAGAAGCUUCCG 53.93%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 53.19%
Apta_520 RNA GGGAGAUCUACGGAUCUCAGGGCUCUUACGGGAGCUACAUGGAAGGAGUCCAUGUGU 52.50%
Apta_718 RNA GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG 52.50%
Apta_1222 RNA GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC 52.00%
Apta_2 RNA GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC 51.25%
Apta_53 RNA UCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGU 51.25%
Apta_81 RNA GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA 51.25%
Apta_256 RNA GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU 51.25%
Apta_453 RNA GGGCUAGCUGAUCGUACCAGUAGCGUGGCCUGGGGGGCCUAGUCGUGCGAUACUAACAGCUAACACCC 51.25%

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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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