Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 684
Aptamer sequence: TTCAAGACGATGCCTGGCGCGAGTTACACACTTGCATGGAGCTGG
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_641 B7 Molecule LPS core 61 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: TTCAAGACGATGCCTGGCGCGAGTTACACACTTGCATGGAGCTGG
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_641 Description B7
Aptamer chemistry DNA Length 45 nt
GC content 55.6% Molecular weight 13,901.92 Da
Molarity of 1 μg/μl solution 71.93 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence TTCAAGACGATGCCTGGCGCGAGTTACACACTTGCATGGAGCTGG
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 684
Target type Molecule
Target unique ID 53481794
Activity 61 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_693 DNA CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG 60.00%
Apta_778 DNA GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC 57.78%
Apta_778 DNA GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC 57.78%
Apta_308 DNA TGGCGGTACGGGCCGTGCACCCACTTACCTGGGAAGTGA 55.56%
Apta_436 DNA CCCCCGCATCACGCCGTGGTGCGATTGACACAATTGCAAT 55.56%
Apta_873 DNA CCACCGAGCCTACCACATGTGACATCCCAGGACATAGCTG 55.56%
Apta_1270 DNA GTATATCAAGCATCGCGTGTTTACACATGCGAGAGGTGAA 55.56%
Apta_1126 DNA TCGGGCGAGTCGTCTGCGGGCGGATAGACTACGACACCGCATCGTCCTCCC 54.90%
Apta_1044 DNA TTTAACGTAACCTGCAAGGCGGGGAGGTGCGAGCCCCGTGTGTGGCTTGC 54.00%
Apta_49 DNA CTTCCATGTTGAGGCGTTTATACCAGTTATCATCGGACTA 53.33%
Apta_259 DNA GCAAGTATGAGCGCAGGAGTTAGGTCCCGTGGCGATGGGT 53.33%
Apta_375 DNA TTGGGGAGGGGCACTGGGCAGTGTAATTTACGAAAGCGAG 53.33%
Apta_406 DNA AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT 53.33%
Apta_437 DNA TCACAGTCCCGGTGCCGCACTAAAACCCATTGTTGTGCGA 53.33%
Apta_834 DNA CGCAATACCAAAGTGGCGAGAGCGCTGTCTTGAGTGAGTGGTTGG 53.33%
Apta_875 DNA GCCGCGACCATACAACGCAAACAACACGCCTGTACGCTTG 53.33%
Apta_938 DNA TTGCCCACCTCCCTGTGCGGGCCACAGAGCAGCAGTGTCGTG 53.33%
Apta_1032 DNA TGGCAAGAGGGTGTGCTTAAGGTGGACACGGTGGCTTAG 53.33%
Apta_1059 DNA TCGTGACGCCGTGCAGTTACCGATACGAGCCTCGTTTTG 53.33%
Apta_1060 DNA AGCAATATTGCCCGCGCGGGGCCAACTGTCCTCACATGA 53.33%

ABOUT

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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