Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 666
Aptamer sequence: ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT
Target unique ID: 6032
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_625 Aptamer # 13_82 Molecule Kanamycin 5.1 μM 100 mM NaCl, 20 mM Tris-HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, and 1 mM CaCl2 23326761
Structure information of aptamer
Aptamer Sequence: ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT
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_625 Description Aptamer # 13_82
Aptamer chemistry DNA Length 98 nt
GC content 48.0% Molecular weight 30,429.47 Da
Molarity of 1 μg/μl solution 32.86 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT
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
Interaction ID 666
Target type Molecule
Target unique ID 6032
Activity 5.1 μM
Binding Conditions/Buffer

100 mM NaCl, 20 mM Tris-HCl pH 7.6, 2 mM MgCl2, 5 mM KCl, and 1 mM CaCl2
Assay

Specificity tests on the representative of each of the groups of DNA oligonucleotides derived from Capture-SELEX against the mixture of pharmaceuticals
PubMed ID 23326761
Interaction ID 1315
Target type Molecule
Target unique ID 6032
Activity 5.1 μM
Binding Conditions/Buffer

10 mmol L-1 Tris-HCl pH 7.5, 1 mmol L-1 EDTA, 2 mol L-1 NaCl
Assay

Specificity tests on the representative of each of the groups of DNA oligonucleotides derived from Capture-SELEX against the mixture of pharmaceuticals
PubMed ID 24566637
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_625 DNA ATACCAGCTTATTCAATTCAGGGCGGTATGAGGCTCGATCAAGGTCGGAGCGAGAATTTTTTCGCGGAGTCGGCTGGATCAGATAGTAAGTGCAATCT
100.00%
Apta_627 DNA ATACCAGCTTATTCAATTATGCGGGGATGAGGCTTGATCTGTGGCTCTGATCCATGATCAGTCGTCTTACGTGCGGTCCAGATAGTAAGTGCAATCT 71.43%
Apta_627 DNA ATACCAGCTTATTCAATTATGCGGGGATGAGGCTTGATCTGTGGCTCTGATCCATGATCAGTCGTCTTACGTGCGGTCCAGATAGTAAGTGCAATCT 71.43%
Apta_626 DNA ATACCAGCTTATTCAATTGGTGGTAGGATGGGCTCGATCGAGGTCTTCAGTCGGCTCGGTTTAGTTTATGTTCTCCTGTAGATAGTAAGTGCAATCT 70.41%
Apta_628 DNA ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT 70.41%
Apta_628 DNA ATACCAGCTTATTCAATTAGCCCGGTATTGAGGTCGATCTCTTATCCTATGGCTTGTCCCCCATGGCTCGGTTATATCCAGATAGTAAGTGCAATCT 70.41%
Apta_626 DNA ATACCAGCTTATTCAATTGGTGGTAGGATGGGCTCGATCGAGGTCTTCAGTCGGCTCGGTTTAGTTTATGTTCTCCTGTAGATAGTAAGTGCAATCT 70.41%
Apta_1016 DNA ATACCAGCTTATTCAATTTCTTCGCCAGTGCCAGGATCTCAGTTGGCGGTTCATTAGCTGGGTTGGTCGAAGATAGTAAGTGCAATCT 69.39%
Apta_805 DNA ATACCAGCTTATTCAATTAGGCGGTGCATTGTGGTTGGTAGTATACATGAGGTTTGGTTGAGACTAGTCGCAAGATATAGATAGTAAGTGCAATCT 67.35%
Apta_450 DNA ATACCAGCTTATTCAATTACATGTCCTGAAGGGGAATAATATACAGCTTTGGGTGGGTAGATAGTAAGTGCAATCT 66.33%
Apta_451 DNA ATACCAGCTTATTCAATTGAGTAAGAGTGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCAATCT 65.31%
Apta_452 DNA ATACCAGCTTATTCAATTGAAGAGTATAAAAAGAGTGATTATCTTTTGTAGGTTTTTTAGATAGTAAGTGCAATCT 64.29%
Apta_727 DNA ATACCAGCTTATTCAATTAGTCACACTTAGAGTTCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGATAGTAAGTGCAATCT 64.29%
Apta_1015 DNA ATACCAGCTTATTCAATTGACCCGTTTCGTTCCCTCTGGGAAGTTTAGCCCAGTTGCCTGGGCGATACCAAGATAGTAAGTGCAATCT 64.29%
Apta_349 DNA ATACCAGCTTATTCAATTAGACGAGTTTTATTCATTTTCCATGTCGTAGCTTACCGTGAGATAGTAAGTGCAATCT 62.24%
Apta_792 DNA ATACCAGCTTATTCAATTCCCAAATTGCCACCACTTACAGCATGATAACATACTACATCTTTTCATCAAGATAGTAAGTGCAATCT 62.24%
Apta_354 DNA ATACCAGCTTATTCAATTCTATACTCCACTTTGCTATTTCTCGGTTCCTTCACGCGCCGATCGCAGGCTGATGAATTGAGATAGTAAGTGCAATCT 61.22%
Apta_1217 DNA ATACGAGCTTGTTCAATACGAAGGGATGCCGTTTGGGCCCAAGTTCGGCATAGTGTGGTGATAGTAAGAGCAATC 61.22%
Apta_583 DNA GTACCAGCTTATTCAATTGCGAGCAGGGTCAATGGAATTAATGATCAATTGACAGACGCAAGTCTCCTGCGGTCCTGTGTTGAGATAGTATGTTCATCAG 61.00%
Apta_823 DNA GGGATACCAGCTTATTCAATTTGATTCCATCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGGTTACGTATTTGGTTTATAGATAGTAAGTGCAATCT 59.60%

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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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