Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 682
Aptamer sequence: CTAAGCACAGGGAAACCAGCTAATGAGTTAGGCCTGTCCCCCACG
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_639 B5 Molecule LPS core 484 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: CTAAGCACAGGGAAACCAGCTAATGAGTTAGGCCTGTCCCCCACG
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_639 Description B5
Aptamer chemistry DNA Length 45 nt
GC content 55.6% Molecular weight 13,808.89 Da
Molarity of 1 μg/μl solution 72.42 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence CTAAGCACAGGGAAACCAGCTAATGAGTTAGGCCTGTCCCCCACG
Applications Detection of endotoxin
Target information
Type Detail Type Detail
PubChem ID 53481794 Molecular name LPS core
Molecular formula C175H317N5O101P6 Molecular weight 4293
IUPAC name (2R,4R,5S,6R)-2-[(2R,4R,5S,6R)-5-[(3S,4R,5R,6R)-4-[(3S,4S,5R,6R)-4-[(3R,4S,5R,6R)-4-[(2R,3R,4S,5R,6R)-3-[(3R,4S,5S,6R)-3-[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3,5-dihydroxy-6-[[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxy-6-[(1S)-2-[(3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-5-phosphonooxyoxan-2-yl]oxy-1-hydroxyethyl]-3,5-dihydroxyoxan-2-yl]oxy-5-[[2-aminoethoxy(hydroxy)phosphoryl]oxy-hydroxyphosphoryl]oxy-6-[(1S)-1,2-dihydroxyethyl]-3-hydroxyoxan-2-yl]oxy-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-2-[[(2R,3S,4R,5R,6R)-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2R,3S,4R,5R,6R)-3-hydroxy-5-[[(3R)-3-hydroxytetradecanoyl]amino]-4-[(3R)-3-hydroxytetradecanoyl]oxy-6-phosphonooxyoxan-2-yl]methoxy]-3-phosphonooxy-4-[(3R)-3-tetradecanoyloxytetradecanoyl]oxyoxan-2-yl]methoxy]oxan-4-yl]oxy-4-[(2R,4R,5R,6R)-4-[2-aminoethoxy(hydroxy)phosphoryl]oxy-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxane-2-carboxylic acid InChIKey AAXCQFOXUJMCCW-PETQGJDISA-N
LogP -5.141 Topological polar surface area 1673.8
Hydrogen bond acceptor 91 Hydrogen bond donor 53

Synonym(s):
LPS core; Endotoxin LPS core; Ra-LPS; Lipopolysaccharide Ra component; Endotoxin Lipopolysaccharide core; Lipopolysaccharide core endotoxin; CHEBI:89983

Activity data

No relevant experimental diagram

 Interaction ID 682
Target type Molecule
Target unique ID 53481794
Activity 484 nM
Binding Conditions/Buffer

50 mM Tris-acetate, pH 8.2
Assay

N/A
PubMed ID 22370280
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1269 DNA TAGCACACAACCCTTTGATTGGGATATCTCATCCCTCG 57.78%
Apta_343 DNA AACAGAGGGACAAACGGGGGAAGATTTGACGTCGACGAC 55.56%
Apta_1150 DNA CTAAGCAGGAAGGTATGGATTGGTTGCATTAG 55.56%
Apta_663 DNA CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG 55.00%
Apta_1045 DNA GGTGCTCAGGGAACTGTCTGAGGGATCAGGCTTAAGCCTGTCGAGCAGTT 54.00%
Apta_981 DNA TATGGAGAGTCAATGAGTACAGTCTCGTCTCAATAACGGAGCCTCGTCCGTGCCCCCG 53.45%
Apta_1218 DNA CGACACCACACAGCAGTAAGCACTACAACATAGTGGTCTAGACTATCTCGGGCCGGTG 53.45%
Apta_586 DNA GGGAGACAAGGAAAATCCTTCAATGAAGTGGGTCGACA 53.33%
Apta_684 DNA GGCGGACCAAGGGGACACCACAGATGAATGTACAGTACCATGTTACTGCGCCCGTAGGTG 53.33%
Apta_883 DNA CGTACCGGCCAGTGATTACGACGAGACGAGCTTATGCGTATTGATGCCTAACTATCTACA 53.33%
Apta_1266 DNA GCATCACACACCGATACTCACCCGCCTGATTAACATTAGCCCACCGCCCACCCCCGCTGC 53.33%
Apta_1265 DNA CACGCACACAACAGCCAATAATGTATAACGCTGTCCACTGTGTGGTGTCCCCCGCGTCG 52.54%
Apta_1087 DNA CTTACGACTCAGGCATTTTGCCGGGTAACGAAGTTACTGTCGTAAG 52.17%
Apta_1213 DNA GGACTTGAAGAAAAGGGCGACACGCGAAGTCGATGTCGCGTCTGCCTGAAGTCA 51.85%
Apta_664 DNA CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA 51.67%
Apta_1228 DNA GGCCACCAAACCACACCGTCGCAACCGCGAGAACCGAAGTAGTGATCATGTCCCTGCGTG 51.67%
Apta_1232 DNA GGCCACACAAACAACATGACAACACGTCTCACATAACGCCCACGTGCTGCCGCCTCATCG 51.67%
Apta_434 DNA ACACGACGGGAATACTGACTCTCCCCCATGT 51.11%
Apta_439 DNA TAACACTCGATTCTCCTAGCCCGCTAGAAATTCCCCTCCC 51.11%
Apta_868 DNA CCCAGAAACAGCACCCTTACATCGACTGGACCTTCCGCG 51.11%

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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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