Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 680
Aptamer sequence: TAGCCGGATCGCGTTGGCCAGATGATATAAAGGGTCAACCCCCCA
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_637 B3 Molecule LPS core 32 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: TAGCCGGATCGCGTTGGCCAGATGATATAAAGGGTCAACCCCCCA
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_637 Description B3
Aptamer chemistry DNA Length 45 nt
GC content 55.6% Molecular weight 13,839.90 Da
Molarity of 1 μg/μl solution 72.25 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence TAGCCGGATCGCGTTGGCCAGATGATATAAAGGGTCAACCCCCCA
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 680
Target type Molecule
Target unique ID 53481794
Activity 32 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_635 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCA
97.78%
Apta_636 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA
95.56%
Apta_638 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCG
95.56%
Apta_965 DNA CACGGCATGTGTGGCCGGATGCCTATATCGGTCGACTGCA 60.00%
Apta_393 DNA AGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 55.56%
Apta_179 DNA TCGGTTGAGTGAGATTAGTCAAATGTTTAGAAGACAACCTC 53.33%
Apta_392 DNA GGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 53.33%
Apta_1126 DNA TCGGGCGAGTCGTCTGCGGGCGGATAGACTACGACACCGCATCGTCCTCCC 52.94%
Apta_980 DNA AACGAGCACGCTTTGTGTACAGCCACTAAATAAGGTATGTAGTCAGCACCCTCGTAAC 51.72%
Apta_1279 DNA TTCCAAGACCTGACCGTAATCGTCAAATGTGTTATTGGAGGGGGACTAGCCCCCGGAGGG 51.67%
Apta_73 DNA GGGGAGTAGGTTGGTGTGGTTGGGGCTCCCC 51.11%
Apta_359 DNA GGGAACGCGTTATTGGGTAACTTCCC 51.11%
Apta_438 DNA AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_439 DNA TAACACTCGATTCTCCTAGCCCGCTAGAAATTCCCCTCCC 51.11%
Apta_438 DNA AGCCATGACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_444 DNA AGCCATTACGATGTCGTTACGTAGATGCAGAGACTCCTAA 51.11%
Apta_445 DNA AGCCATGACGATGTCGTTACGTAGATGTAGAGACTCCTAA 51.11%
Apta_446 DNA AGCCATGACGATGTCGTTACGTAGATGCATAGACTCCTAA 51.11%
Apta_580 DNA ATGCGGGTATATGGTGCGAGAAAACAAGGGGCATACTGGA 51.11%
Apta_778 DNA GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC 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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