Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 685
Aptamer sequence: ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_642 B8 Molecule LPS core 71 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA
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_642 Description B8
Aptamer chemistry DNA Length 45 nt
GC content 46.7% Molecular weight 13,846.94 Da
Molarity of 1 μg/μl solution 72.22 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence ATCCAATACCTCAGAACTCAGTTCGAGTCGTAAAGGGGAATCGCA
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 685
Target type Molecule
Target unique ID 53481794
Activity 71 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_142 DNA CGCACATCAGTTTAGCAGCGCCAAAGGCGGAAGCGCA 57.78%
Apta_273 DNA ATAAGCTGAGCATCTTAGATCCCCGTCAAGGGCAGCGTAA 55.56%
Apta_1172 DNA GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA 54.39%
Apta_385 DNA ACAGATACGGAACTACAGAGGTCAATTACGGTGGCCACGC 53.33%
Apta_578 DNA CACCAAGCGCAGGGAATTACATTGAAGTGTGGGATTGGCT 53.33%
Apta_1191 DNA TAATACTACCAACTTCTTTGCCTGGCGTAAGTAACAGTCA 53.33%
Apta_309 DNA TAGCCAAGGTAACCAGTACAAGGTGCTAAACGTAATGGCTTCGGCTTAC 53.06%
Apta_309 DNA TAGCCAAGGTAACCAGTACAAGGTGCTAAACGTAATGGCTTCGGCTTAC 53.06%
Apta_621 DNA AAGCTTGCTTTATAGCCTGCAGCGATTCTTGATCGGAAAAGGCTGAGAGCTACGC 52.73%
Apta_990 DNA AACCCAACCCCGCACCATTAGTCTAAATTTTCGCGACGGAACACAGCAACAACTCCCCA 52.54%
Apta_794 DNA ATCCAGAGTGACGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGACACGGTGGCTTAGT 52.05%
Apta_395 DNA AATCCACGTATCGACTAGCTCAAACCAGCCTGATAGAGCCATTCGCTTTA 52.00%
Apta_972 DNA TGACAGTACGTACTGAACTAATTTATAAGTAATTTGCTATGGTGGTATCC 52.00%
Apta_976 DNA GATGAATATCGCAATGAAATTATATATGTATAATTGGAACGGTGGTATCC 52.00%
Apta_977 DNA CAATCTGCTAAAACTTAAAGCCTATTAATGAAATTGTTAAGGTGGTATCC 52.00%
Apta_1042 DNA ATCACGATATGCCCGGCTCATCGGGGTTCAGTTGGGCGGTCACATGGAAA 52.00%
Apta_1047 DNA TAGTCCCAAGGCACATAAGGGCCGGAGGTCTAGCGTCAGGGATACAGAGA 52.00%
Apta_1279 DNA TTCCAAGACCTGACCGTAATCGTCAAATGTGTTATTGGAGGGGGACTAGCCCCCGGAGGG 51.67%
Apta_1169 DNA TTTTTTTTTTTCAGCACCGACCTTGTGCTTTGGGAGTGCTGGTCCAAGGGCGTTAATGGACA 51.61%
Apta_923 DNA ATCCAGAGTGACGCAGCATCGACCTCTGTGCGAGCGGGTTGCATATATATTTTGCATGGACACGGTGGCTTAGT 51.35%

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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