Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 581
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Target unique ID: 3081545
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_548 LS13 Molecule Apramycin 35.9 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 3081545 Molecular name Apramycin
Molecular formula C21H41N5O11 Molecular weight 539.6
IUPAC name (2R,3R,4S,5S,6S)-2-[[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy-4-hydroxy-3-(methylamino)-2,3,4,4a,6,7,8,8a-octahydropyrano[3,2-b]pyran-2-yl]oxy]-5-amino-6-(hydroxymethyl)oxane-3,4-diol InChIKey XZNUGFQTQHRASN-XQENGBIVSA-N
LogP -6.949 Topological polar surface area 283.64
Hydrogen bond acceptor 16 Hydrogen bond donor 11

Synonym(s):
apramycin; 37321-09-8; Nebramycin II; Nebramycin factor 2; Apramycinum; Apramicina; Apramycine; UNII-388K3TR36Z; CHEBI:2790; (2R,3R,4S,5S,6S)-2-[[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy-4-hydroxy-3-(methylamino)-2,3,4,4a,6,7,8,8a-octahydropyrano[3,2-b]pyran-2-yl]oxy]-5-amino-6-(hydroxymethyl)oxane-3,4-diol; 4-O-((8R)-2-Amino-8-O-(4-amino-4-deoxy-alpha-D-glucopyranosyl)-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranos-1-yl)-2-deoxy-D-streptamine; 4-O-(3alpha-Amino-6alpha-((4-amino-4-deoxy-alpha-D-glucopyranosyl)oxy)-2,3,4,5abeta,6,7,8,8aalpha-octahydro-8beta-hydroxy-7beta-(methylamino)pyrano(3,2-b)pyran-2alpha-yl)-2-deoxy-D-streptamine; 388K3TR36Z; EL-857; Ambylan; Apralan; (2R,3R,4S,5S,6S)-5-Amino-2-(((2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-(((1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl)oxy)-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol; (2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yl 4-amino-4-deoxy-alpha-D-glucopyranoside; AM2; Apramycine [INN-French]; Apramycinum [INN-Latin]; Apramicina [INN-Spanish]; Apramycin [USAN:INN:BAN]; NCGC00016836-01; EINECS 253-460-1; CAS-37321-09-8; EL 857; Apramycin (USAN/INN); EL-857/820; DSSTox_CID_25465; DSSTox_RID_80896; DSSTox_GSID_45465; SCHEMBL18388; CHEMBL1230961; DTXSID5045465; GTPL10760; EL857; HMS2090I15; D-Streptamine, O-4-amino-4-deoxy-alpha-D-glucopyranosyl-(1-8)-O-(8R)-2-amino-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octadialdo-1,5:8,4-dipyranosyl-(1-4)-2-deoxy-; ZINC8214486; Tox21_110639; DB04626; NSC 758938; HY-17558; O211; C01555; D02322; AB01275497-01; Apramycin, Antibiotic for Culture Media Use Only; A936645; Q418940; W-106548; UNII-NQJ13I4Z9U component XZNUGFQTQHRASN-XQENGBIVSA-N; (2R,3R,4S,5S,6S)-5-amino-2-((2R,3S,4R,4aR,6S,7R)-7-amino-6-((1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyloxy)-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yloxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol; (2R,3R,4S,5S,6S)-5-amino-2-{[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yl]oxy}-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (non-preferred name); D-Streptamine, 4-O-((8R)-2-amino-8-O-(4-amino-4-deoxy-alpha-D-glucopyranosyl)-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranos-1-yl)-2-deoxy-; D-Streptamine, O-4-amino-4-deoxy-alpha-D-glucopyranosyl-(1.fwdarw.8)-O-(8R)-2-amino-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranosyl-(1.fwdarw.4)-2-deoxy-; NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-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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