Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 755
Aptamer sequence: ACGTTGACGCTGGTGCCCGCTTGTGGTGCGAGTGTTGTGT
Target unique ID: 54675779
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_692 No. 5 Molecule Oxytetracycline 12.08 nM 100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6 17988875
Structure information of aptamer
Aptamer Sequence: ACGTTGACGCTGGTGCCCGCTTGTGGTGCGAGTGTTGTGT
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_692 Description No. 5
Aptamer chemistry DNA Length 40 nt
GC content 60.0% Molecular weight 12,412.92 Da
Molarity of 1 μg/μl solution 80.56 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence ACGTTGACGCTGGTGCCCGCTTGTGGTGCGAGTGTTGTGT
Applications Binding to oxytetracycline (OTC)
Target information
Type Detail Type Detail
PubChem ID 54675779 Molecular name Oxytetracycline
Molecular formula C22H24N2O9 Molecular weight 460.4
IUPAC name (4S,4aR,5S,5aR,6S,12aR)-4-(dimethylamino)-1,5,6,10,11,12a-hexahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide InChIKey OWFJMIVZYSDULZ-PXOLEDIWSA-N
LogP -1.4 Topological polar surface area 201.85
Hydrogen bond acceptor 10 Hydrogen bond donor 7

Synonym(s):
oxytetracycline; Terramycin; 79-57-2; Oxyterracine; Oxytetracyclin; Oxymycin; Terrafungine; Oxyterracin; Oxitetraciclina; Oxitetracyclin; Adamycin; Biostat; Geomycin; Ryomycin; Oxitetracyclinum; Oxytetracyclinum; Oxytetracycline (anhydrous); Oxyterracyne; Oxytetracycline anhydrous; Solkaciclina; Dabicycline; Fanterrin; Geotilin; Imperacin; Lenocycline; Oksisyklin; Proteroxyna; Riomitsin; Terramitsin; Ursocyclin; Ursocycline; Oxypam; Tarocyn; Tarosin; Teravit; Tetran; Antibiotic TM 25; Oxytetracycline amphoteric; 5-Hydroxytetracycline; Liquamycin LA 200; Biostat PA; Bisolvomycin; Oxysteclin; Oxymykoin; Vendarcin; Ossitetraciclina; Pennox 200; Oxytetracycline (Terramycin); Oxytetracycline [INN]; Berkmycen; Mycoshield TMQTHC 20; Oxytetracycline base; Dalimycin; Oxacycline; Unimycin; NSC-9169; Oxytetracycline calcium; Stevacin; Macocyn; Medamycin; Oxy-Kesso-tetra; 6153-64-6; UNII-SLF0D9077S; Mepatar; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide; OTC (antibiotic); MLS000069429; SLF0D9077S; Tetracycline, 5-hydroxy-; CHEBI:27701; Oxytetracycline (internal use); Stecsolin; Oxydon; TM 5; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-, (4S,4aR,5S,5aR,6S,12aS)-; Oxytetracid; E703; NCI-C56473; SMR000059000; Terramycin im; NSC 9169; Terramycin Q50; Q63393012; Ossitetraciclina [DCIT]; Oxytetracyclinum [INN-Latin]; Oxitetraciclina [INN-Spanish]; Terramicina Oftalmica; 79-57-2 (ANHYDROUS); Geomycin (Streptomyces vimosus); HSDB 3145; EINECS 201-212-8; LA 200; BRN 2714587; Embryostat; Galsenomycin; Oxitetracycline; SR-01000003006; Hydroxytetracyclinum; Oxytetracycline,(S); 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-, (4S-(4alpha,4aalpha,5alpha,5aalpha,6beta,12aalpha))-; 5-Hydroxy-Tetracycline; Spectrum_001055; Opera_ID_661; Prestwick0_000307; Prestwick1_000307; Prestwick2_000307; Prestwick3_000307; Spectrum2_000988; Spectrum3_000536; Spectrum4_000466; Spectrum5_001148; Oxytetracycline(Terramycin); SCHEMBL2899; CHEMBL1517; DSSTox_CID_14260; DSSTox_RID_79133; DSSTox_GSID_34260; BSPBio_000274; BSPBio_002151; KBioGR_000912; KBioSS_001535; 4-14-00-02633 (Beilstein Handbook Reference); DivK1c_000225; SCHEMBL560497; SPBio_001055; SPBio_002493; BPBio1_000302; CHEMBL461529; CHEMBL1401333; CHEMBL4280957; DTXSID1034260; NSC9169 (HCL); SCHEMBL13169109; SCHEMBL13782651; GTPL10919; KBio1_000225; KBio2_001535; KBio2_004103; KBio2_006671; KBio3_001651; 6153-64-6 (di-hydrate); NINDS_000225; BDBM241973; (4S,4aR,5S,5aR,6S,12aR)-4-(dimethylamino)-1,5,6,10,11,12a-hexahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide; HY-B0275; 2058-46-0 (mono-hydrochloride); Tox21_302380; LMPK07000005; MFCD00003700; s1773; ZINC95626782; AKOS015951277; AKOS015961254; ZINC100026355; ZINC100303028; CCG-269334; DB00595; MCULE-5398230579; CAS-79-57-2; IDI1_000225; NCGC00091268-04; NCGC00091268-05; NCGC00091268-06; NCGC00091268-07; NCGC00091268-08; NCGC00091268-09; NCGC00091268-11; NCGC00091268-12; NCGC00188956-01; NCGC00255168-01; AC-12777; AC-13466; S470; 7179-50-2 (calcium (1:1) salt); SBI-0051473.P003; SW196796-3; 3,5,6,10,12,12a-hexahydroxy-6-methyl-; C06624; E75911; Oxytetra Selective Supplement, for microbiology; AB00053514_04; AB00053514_05; AB01274728-01; AB01274728_02; 135740-EP2275422A1; 135740-EP2292608A1; 6153-65-7 (di-hydrochloride salt, di-hydrate); A839720; Q411646; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-; SR-01000003006-5; 1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene; Oxytetracycline, British Pharmacopoeia (BP) Reference Standard; Oxytetracycline, European Pharmacopoeia (EP) Reference Standard; (4S,4aR,5S,5aR,6S,12aS)-4-(dimethylamino)-3,5,6,10,12,12a-hexahydroxy-6-methyl-1,11-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide

Activity data
Interaction ID 755
Target type Molecule
Target unique ID 54675779
Activity 12.08 nM
Binding Conditions/Buffer

100 mM NaCl, 20 mM Tris-HCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02 Tween 20, pH 7.6
Assay

Binding of ssDNA aptamers to oxytetracycline (OTC) was performed by equilibrium dialysis as described in methods
PubMed ID 17988875
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 62.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 62.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 62.50%
Apta_1203 DNA CCCTGCGGGGCTACCCGATATGTGTCCGAGTGGTG 62.50%
Apta_1199 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAAGTGGTG 62.50%
Apta_1208 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAGGTGGTG 62.50%
Apta_350 DNA GGTGGTGGTGGTTGTGGTGGTGGTGG 60.00%
Apta_1240 DNA GGAGTAGTGGGGATTGTGGTGTATGTTGTC 60.00%
Apta_577 DNA ACTTCAGTGAGTTGTCCCACGGTCGGCGAGTCGGTGGTAG 57.50%
Apta_693 DNA CGAGTTGAGCCGGGCGCGGTACGGGTACTGGTATGTGTGG 57.50%
Apta_945 DNA GTTAGACGCTGGACCGCGTGTGATCGGGTCAGCTGCAATT 57.50%
Apta_1059 DNA TCGTGACGCCGTGCAGTTACCGATACGAGCCTCGTTTTG 57.50%
Apta_1239 DNA GGTGGATGGGGATGCTTTGTTAGTTTGTGC 57.50%
Apta_1245 DNA AGTGTGAAGTGGTGTGTGTTGTTGTTTGTC 57.50%
Apta_1257 DNA CGACGCACAGTCGCTGGTGCGTACCTGGTTGCCGTTGTGT 57.50%
Apta_1261 DNA GGGCGGACGCTAGGTGGTGATGCTGTGCTACACGTGTTGT 57.50%
Apta_910 DNA TCACGTGCATGATAGACGGCGAAGCCGTCGAGTTGCTGTGTGCCGATGCACGTGA 56.36%
Apta_882 DNA AATAGTCTGGTTCGGTGCTTGGTGCGATGTGTTAGTCAGACTCTTGTGTG 56.00%
Apta_821 DNA CACAGTCACTCAGACGGCCGCTATTGTTGCCAGATTGCCTTTGGC 55.56%
Apta_835 DNA TATGGCGTGGCAAGCTTGGCCCGCTTCTCAAGCATGGTTATCTAC 55.56%

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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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