Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 679
Aptamer sequence: TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA
Target unique ID: 53481794
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_636 B2 Molecule LPS core 12 nM 50 mM Tris-acetate, pH 8.2 22370280
Structure information of aptamer
Aptamer Sequence: TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA
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_636 Description B2
Aptamer chemistry DNA Length 45 nt
GC content 60.0% Molecular weight 13,840.89 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 TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA
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 679
Target type Molecule
Target unique ID 53481794
Activity 12 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_637 DNA TAGCCGGATCGCGTTGGCCAGATGATATAAAGGGTCAACCCCCCA
95.56%
Apta_638 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCG
95.56%
Apta_965 DNA CACGGCATGTGTGGCCGGATGCCTATATCGGTCGACTGCA 60.00%
Apta_393 DNA AGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 55.56%
Apta_1126 DNA TCGGGCGAGTCGTCTGCGGGCGGATAGACTACGACACCGCATCGTCCTCCC 54.90%
Apta_392 DNA GGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 53.33%
Apta_439 DNA TAACACTCGATTCTCCTAGCCCGCTAGAAATTCCCCTCCC 53.33%
Apta_593 DNA CTCTCGGGACGACAGCCGAGTTGATTCAACAGCCGAGTCGTCCC 53.33%
Apta_664 DNA CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA 53.33%
Apta_722 DNA CTCTCGGGACGACGGCCCGATCTCAGAGTAGTCGTCCC 53.33%
Apta_939 DNA TTGCCCACCGTACTGTGCAGGTCGAACTACAGGCACGTCGTG 53.33%
Apta_1279 DNA TTCCAAGACCTGACCGTAATCGTCAAATGTGTTATTGGAGGGGGACTAGCCCCCGGAGGG 53.33%
Apta_721 DNA CTCTCGGGACGACCGCGGTAGTCTTAACCTAAAGCGGTGTCAGGTCGTCCC 52.94%
Apta_1125 DNA TCGGGCGAGTCGTCTGGGGAGGTCAGAACGAAAGGCCCGCATCGTCCTCCC 52.94%
Apta_1127 DNA TCGGGCGAGTCGTCTGCGAGGCAACAAGCTCGTAATCCGCATCGTCCTCCC 52.94%
Apta_509 DNA TCGCGCGAGTCGTCTGGGGGACTAGAGGACTTGTGCGGCCCCGCATCGTCCTCCC 52.73%
Apta_1272 DNA TCCGTGTATAGGTCGGGTCTCTTGCCAACTGATTCGTTGAAAAGTATAGCCCCGCAGGG 52.54%
Apta_989 DNA ATGCGGGTACATCTCTCCAACCAGTCAAACTGCTATGATAAGACCTCATTCAACCCCGGTA 52.46%
Apta_980 DNA AACGAGCACGCTTTGTGTACAGCCACTAAATAAGGTATGTAGTCAGCACCCTCGTAAC 51.72%

ABOUT

AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

HELP CENTER

>Contact us
>LMMD Group
>School of Pharmacy

DEV TOOL
Page last updated at 2022-05-25 10:01:57 (Asia/Shanghai) | You are visitor No. 43962
Copyright © 2019-2020 Laboratory of Molecular Modeling and Design, School of Pharmacy, East China University of Science and Technology. All rights reserved.