Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 778
Aptamer sequence: CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU
Target unique ID: 643990
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_705 5 Molecule Sialyl-Lewis X 0.085 nM 150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2 11178986
Structure information of aptamer
Aptamer Sequence: CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU
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_705 Description 5
Aptamer chemistry RNA Length 133 nt
GC content 46.6% Molecular weight 42,804.31 Da
Molarity of 1 μg/μl solution 23.36 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU
Applications Inhibition of the cell adhesion
Target information
Type Detail Type Detail
PubChem ID 643990 Molecular name Sialyl-Lewis X
Molecular formula C31H52N2O23 Molecular weight 820.7
IUPAC name (2S,4S,5R,6R)-5-acetamido-2-[(2S,3R,4S,5S,6R)-2-[(2R,3R,4R,5R)-5-acetamido-1,2-dihydroxy-6-oxo-4-[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyhexan-3-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid InChIKey LAQPKDLYOBZWBT-NYLDSJSYSA-N
LogP -9.385 Topological polar surface area 410.71
Hydrogen bond acceptor 22 Hydrogen bond donor 15

Synonym(s):
Sialyl-Lewis X; SLex; 98603-84-0; 3'-Sialyl-Lewis X; sialyl Lewis x; SialylLewisX; sialyl LewisX; Sialyl lewis-x; Sialyl Lex tri; 3'-Sialyl-Lewis-X tetrasaccharide; Sialyl LeX; 3'-SIALYL LEWIS X; 3'-SLeX; SSEA 1; UNII-0PS35WG8U3; 0PS35WG8U3; (2S,4S,5R,6R)-5-acetamido-2-[(2S,3R,4S,5S,6R)-2-[(2R,3R,4R,5R)-5-acetamido-1,2-dihydroxy-6-oxo-4-[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyhexan-3-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid; a-NeuNAc-(2>3)-b-D-Gal-(1>4)(a-L-Fuc-[1>3])-D-GlcNAc; 3-Sialyl Lewis X; SCHEMBL346849; CHEMBL375586; DTXSID60913167; BDBM50450369; ZINC96129530; HY-W020790; CS-0031944; J3.549.354I; Q3959958; W-204175; alpha-NeuNAc-(2>3)-beta-delta-Gal-(1>4)(a-L-Fuc-[1>3])-delta-GlcNAc; (2S,4S,5R,6R)-5-acetamido-2-{[(2S,3R,4S,5S,6R)-2-{[(2R,3R,4R,5R)-5-acetamido-1,2-dihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid; 6-Deoxyhexopyranosyl-(1->3)-[3,5-dideoxy-5-[(1-hydroxyethylidene)amino]non-2-ulopyranonosyl-(2->3)hexopyranosyl-(1->4)]-2-deoxy-2-[(1-hydroxyethylidene)amino]hexose; D-Glucose, O-(N-acetyl-a-neuraminosyl)-(2>3)-O-b-D-galactopyranosyl-(1>4)-O-[6-deoxy-a-L-galactopyranosyl-(1>3)]-2-(acetylamino)-2-deoxy- (9CI); D-Glucose, O-(N-acetyl-alpha-neuraminosyl)-(2->3)-o-beta-D-galactopyranosyl-(1->4)-O-(6-deoxy-alpha-L-galactopyranosyl-(1->3))-2-(acetylamino)-2-deoxy-; D-glucose, O-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-2-nonulopyranonosyl-(2>3)-O-beta-D-galactopyranosyl-(1>4)-O-[6-deoxy-alpha-L-galactopyranosyl-(1>3)]-2-(acetylamino)-2-deoxy-

Activity data
Interaction ID 778
Target type Molecule
Target unique ID 643990
Activity 0.085 nM
Binding Conditions/Buffer

150 mM NaCl, 20 mM Hepes (pH 7.4), 1 mM CaCl2, 1 mM MgCl2
Assay

Inhibition of the HL60 cell adhesion to E-selectin and P-selectin
PubMed ID 11178986
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_280 RNA GAUAAUACGACUCACUAUAGGGUUCACUGCAGACUUGACGAAGCUUGCAGAAAAGGGGGAAGAAGAGGGUGAUUCAGGCGAGAGAAUGGAUCCACAUCUACGAAUUC 54.14%
Apta_557 RNA GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG 52.63%
Apta_874 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC 52.63%
Apta_169 RNA GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUUCGACAUGAGACUCACAACAGUUCCCUUUAGUGAGGGUUAAUU 51.88%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 51.88%
Apta_168 RNA AAUUAACCCUCACUAAAGGGAACUGUUGUGAGUCUCAUGUCGAAGAGCGGUUAAGGGAGAUUUAGGCAGCAGCUUGGACAGUGUAUCGGCUGAGUUGAGCGUCUAGUCUUGUCU 51.13%
Apta_376 RNA GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC 51.13%
Apta_719 RNA GGAAUGGAUCCACAUCUACGAAGGCUUUGAAGGUGAGACCGUGCAAAUGAGGAUGGUGUGGAUGAUUAGGGUUGUCGGUUUUCACUGCAGACUUGACGAAGCUU 51.13%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 51.13%
Apta_909 RNA GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG 51.13%
Apta_936 RNA GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC 51.13%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 50.38%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 50.38%
Apta_559 RNA GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGGAUCAUCGGACUUUGUCCUGUGGAGUAAGAUCGCGAAACGGUGAAAGCCGUAGGUCU 50.38%
Apta_337 RNA GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG 49.62%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 49.62%
Apta_551 RNA GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGCGGUGCUAGUUAGUUGCAGUUUCGGUUGUUACGCGAAACGGUGAAAGCCGUAGGUCU 49.62%
Apta_382 RNA GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC 48.87%
Apta_494 RNA GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU 48.87%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 48.87%

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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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