Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 580
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC
Target unique ID: 3081545
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_547 LGA11 Molecule Apramycin 28.4 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 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 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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