Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 640
Aptamer sequence: CGGUUGGAUGGGUGUUGGUGGUUUGUUGAGUCCAGGCGGC
Target unique ID: 54671203
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_606 VA 22 Molecule Doxycycline 72 nM 20 mM Tris at pH 7.5 with 100 mM NaCl, 2 mM MgCl2, 5 mM KCl and 1 mM CaCl2, RT 28634758
Structure information of aptamer
Aptamer Sequence: CGGUUGGAUGGGUGUUGGUGGUUUGUUGAGUCCAGGCGGC
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_606 Description VA 22
Aptamer chemistry RNA Length 40 nt
GC content 60.0% Molecular weight 12,990.62 Da
Molarity of 1 μg/μl solution 76.98 μM Number of G-quadruplexes 2
G-Score 19 Function Aptasensor
Sequence CGGUUGGAUGGGUGUUGGUGGUUUGUUGAGUCCAGGCGGC
Applications Binding to DOX
Target information
Type Detail Type Detail
PubChem ID 54671203 Molecular name Doxycycline
Molecular formula C22H24N2O8 Molecular weight 444.4
IUPAC name (4S,4aR,5S,5aR,6R,12aR)-4-(dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide InChIKey SGKRLCUYIXIAHR-AKNGSSGZSA-N
LogP -0.504 Topological polar surface area 181.62
Hydrogen bond acceptor 9 Hydrogen bond donor 6

Synonym(s):
doxycycline; 564-25-0; Vibramycin; Doxytetracycline; Doxiciclina; Doxycyclinum; Doxycycline (anhydrous); Monodox; Oracea; Vibra-tabs; Doxycycline hyclate; 6alpha-Deoxy-5-oxytetracycline; 5-Hydroxy-alpha-6-deoxytetracycline; 6-alpha-Deoxy-5-oxytetracycline; Doxycyclin; alpha-6-Deoxy-5-hydroxytetracycline; BMY-28689; Liviatin; DOXY; Doxy-Caps; Vibravenos; UNII-334895S862; Deoxymykoin; Dossiciclina; Azudoxat; Doxitard; Doxivetin; Doxycen; Doxychel; Investin; Ronaxan; CHEBI:50845; Spanor; Doxy-Puren; alpha-Doxycycline; Doxy-Tabs; alpha-6-Deoxyoxytetracycline; MMV000011; (4S,4aR,5S,5aR,6R,12aR)-4-(dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide; Doxycycline anhydrous; Supracyclin; Doxysol; Jenacyclin; 6-Deoxyoxytetracycline; Dossiciclina [DCIT]; Doxiciclina [Italian]; (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide; 2-Naphthacenecarboxamide,4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS)-; Doxycyclinum [INN-Latin]; Doxycycline (internal use); Doxiciclina [INN-Spanish]; 334895S862; BU-3839T; 4-Epidoxycycline; Zenavod; DOXCYCLINE ANHYDROUS; Oxytetracycline, 6-deoxy-; Doxycycline (TN); Doxychel (TN); Vivox (*Hyclate); Doxycycline (INN); DMSC (*Fosfatex); NSC633557; HSDB 3071; Monodox (*monohydrate); BMY28689; BU 3839T; 24390-14-5; EINECS 209-271-1; BMY 28689; Vibramycin (*monohydrate); GS-3065 (*monohydrate); Doxirobe; Doxycycline [USAN:INN:BAN]; SR-01000075844; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS)-; Anhydrous doxycycline; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S-(4alpha,4aalpha,5alpha,5aalpha,6alpha,12aalpha))-; AB08 (*Fosfatex); Spectrum_000807; Spectrum2_000143; Spectrum3_000408; Spectrum4_000527; Spectrum5_000947; UPCMLD-DP021; CHEMBL1433; Lopac0_000405; SCHEMBL40930; SCHEMBL66828; BSPBio_001936; KBioGR_001133; KBioSS_001287; BIDD:GT0146; DivK1c_000345; SPBio_000246; CHEMBL436921; GTPL6464; SCHEMBL1176275; 4-Epioxytetracycline, 6-deoxy-; DTXSID0037653; SCHEMBL17826665; SCHEMBL19270298; SCHEMBL21753474; UPCMLD-DP021:001; BCBcMAP01_000024; KBio1_000345; KBio2_001287; KBio2_003855; KBio2_006423; KBio3_001156; DTXSID80992212; NINDS_000345; HMS2090E06; DOXYTETRACYCLINE; DOXYCYCLINE; HY-N0565; LMPK07000001; s5159; ZINC16052277; AKOS015900372; ZINC100056779; ZINC100302137; ZINC100611210; ZINC109562088; CCG-204498; DB00254; MCULE-4368118692; SDCCGSBI-0050391.P005; IDI1_000345; SMP1_000107; NCGC00161602-01; NCGC00161602-03; NCGC00161602-04; NCGC00161602-05; NCGC00161602-07; NCGC00161602-14; NCGC00188979-01; (4s,4ar,5s,5ar,6r,12as)-4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6R,12aS); 2-Naphthacenecarboxamide, 4-alpha-S-(dimethylamino)-1,4,4a-alpha-5,5a-alpha,6,11,12a-octahydro-3,5-alpha,10,12,12a-alpha-pentahydroxy-6-alpha-methyl-1,11-dioxo-; AS-13499; I455; SBI-0050391.P004; CS-0009105; 1368-EP2269978A2; 1368-EP2269985A2; 1368-EP2269991A2; 1368-EP2284150A2; 1368-EP2284151A2; 1368-EP2284152A2; 1368-EP2284153A2; 1368-EP2284155A2; 1368-EP2284156A2; 1368-EP2284164A2; 1368-EP2287140A2; 1368-EP2287148A2; 1368-EP2287150A2; 1368-EP2289871A1; 1368-EP2295402A2; 1368-EP2295419A2; 1368-EP2298732A1; 1368-EP2301534A1; 1368-EP2301912A2; 1368-EP2301913A1; 1368-EP2301914A1; 1368-EP2301916A2; 1368-EP2305637A2; 1368-EP2305640A2; 1368-EP2308863A1; 1368-EP2311451A1; 1368-EP2311796A1; 1368-EP2311797A1; 1368-EP2311798A1; 1368-EP2311799A1; 1368-EP2316450A1; C06973; D07876; AB00053465-03; AB00053465_04; AB00053465_05; 564D250; A817263; Doxycycline, Antibiotic for Culture Media Use Only; Q422442; SR-01000075844-7; W-105517; SR-01000075844-18; (4S,4aR,5S,5aR,6R,12aS)-4-(DiMethylaMino)-3,5,10,12,12a-pentahydroxy-6-Methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxaMidehydrochloride; (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide; 4-(Dimethylamino)-1,5,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-3,4,4a,5,5a,6,12,12a-octahydrotetracene-2-carboximidic acid; 7164-70-7

Activity data

No relevant experimental diagram

 Interaction ID 640
Target type Molecule
Target unique ID 54671203
Activity 72 nM
Binding Conditions/Buffer

20 mM Tris at pH 7.5 with 100 mM NaCl, 2 mM MgCl2, 5 mM KCl and 1 mM CaCl2, RT
Assay

N/A
PubMed ID 28634758
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_703 RNA GGGCGGAUGAGACGCUUGGCGUGUGCUGUGGAGAGUCAUCCG 54.76%
Apta_402 RNA GCCUGUAAGGUGGUCGGUGUGGCGAGUGUGUUAGGAGAGAUUGC 54.55%
Apta_131 RNA GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA 52.94%
Apta_51 RNA GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC 52.50%
Apta_603 RNA CUUGUCUGAACAAUUUCGUCUGCCUUUGCGUUCCGACGGC 52.50%
Apta_633 RNA GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC 52.50%
Apta_1167 RNA GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC 52.50%
Apta_132 RNA GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA 50.98%
Apta_1143 RNA ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA 50.98%
Apta_218 RNA AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU 50.00%
Apta_231 RNA GGGAGGACGAUGCGGGUGUGGGGCG 50.00%
Apta_242 RNA GCUUCCAGGAAGAGAAGUGUCAUGUGAUCAGUCCUGGUGGGUGG 50.00%
Apta_304 RNA CGGCCGAUAGAAAGACUACUUGAGCCCUUAAAUGAGGUUAUGUGCGGCCG 50.00%
Apta_594 RNA GGGCUAUUGCUGGAGGGGCGCCACAUGAAAGUGGUGGUUGGGUGCGGUCGGCGAUAGCUC 50.00%
Apta_632 RNA GACGAGAAGGAGUGCUGGUUAUACUAGCGGUUAGGUCACUCGUC 50.00%
Apta_925 RNA GCUCGGCCAGGUCGCGGGUGGAUGUGAGGG 50.00%
Apta_1166 RNA GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC 50.00%
Apta_1188 DNA CGGGCGGGGCGTGGGGTGTTGGAGTGGAGGGCGGGGCGGC 50.00%
Apta_718 RNA GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG 49.25%
Apta_520 RNA GGGAGAUCUACGGAUCUCAGGGCUCUUACGGGAGCUACAUGGAAGGAGUCCAUGUGU 49.12%

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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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