Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 782
Aptamer sequence: GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU
Target unique ID: 54675776
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_707 cb28 minimer Molecule Tetracycline 1 μM 10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 250 mM NaCl 11557342
Structure information of aptamer
Aptamer Sequence: GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU
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_707 Description cb28 minimer
Aptamer chemistry RNA Length 60 nt
GC content 50.0% Molecular weight 19,333.56 Da
Molarity of 1 μg/μl solution 51.72 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAGGUGAAGAAUUCGACCACCUAGGCCGGU
Applications Recognizing the tetracycline
Target information
Type Detail Type Detail
PubChem ID 54675776 Molecular name Tetracycline
Molecular formula C22H24N2O8 Molecular weight 444.4
IUPAC name (4S,4aS,5aS,6S,12aR)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide InChIKey NWXMGUDVXFXRIG-WESIUVDSSA-N
LogP -0.371 Topological polar surface area 181.62
Hydrogen bond acceptor 9 Hydrogen bond donor 6

Synonym(s):
tetracycline; 60-54-8; Deschlorobiomycin; Tetracyclinum; Achromycin; Tetracyclin; Sumycin; Abramycin; Tsiklomitsin; Achromycin V; Liquamycin; Panmycin; Tetracyn; Tetrazyklin; Ambramycin; Hostacyclin; Omegamycin; Tetradecin; Tetraverine; Tsiklomistsin; Vetacyclinum; Tetrafil; Tetracycline base; Cefracycline; Criseociclina; Abricycline; Agromicina; Ambramicina; Biocycline; Ciclibion; Copharlan; Democracin; Lexacycline; Limecycline; Mericycline; Micycline; Orlycycline; Polycycline; Polyotic; Purocyclina; Roviciclina; Solvocin; Tetrabon; Tetracycl; Amycin; Veracin; SK-Tetracycline; Tetracycline II; Tetra-Co; Tetracyclinehydrate; UNII-F8VB5M810T; Cyclomycin; Sustamycin; Sumycin syrup; Tetracycline I; Bio-tetra; (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide; CHEBI:27902; Piracaps (base); Centet (base); Polycycline (VAN); 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S,4aS,5aS,6S,12aS)-; Cefracycline suspension; Liquamycin (Veterinary); Polycycline (antibiotic); F8VB5M810T; (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide; Tetraciclina; Tetracycline (internal use); Supramycin; Vetquamycin-324 (free base); MFCD00151232; 60-54-8 (FREE BASE); NSC-108579; E701; Achromycin (naphthacene derivative); NSC 108579; T-125; HSDB 3188; 6-Methyl-1,11-dioxy-2-naphthacenecarboxamide; Tetracyclinum [INN-Latin]; Tetraciclina [INN-Spanish]; (4S,4aS,5aS,6S,12aR)-4-(dimethylamino)-1,6,10,11,12a-pentahydroxy-6-methyl-3,12-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide; Sumycin (TN); 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-, (4S-(4alpha,4aalpha,5aalpha,6beta,12aalpha))-; 6416-04-2 (3H2O); Economycin; Vetquamycin; Brodspec; Tetracycline (JAN/USP/INN); CCRIS 9483; SR-01000000212; NSC108579; Tetrabid Organon; Ala-Tet; Tetracycline [USP:INN:BAN:JAN]; 2-Naphthacenecarboxamide, 4-(dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-; EINECS 200-481-9; Spectrum_001034; Tetracycline, EP grade; Prestwick0_000140; Prestwick1_000140; Prestwick2_000140; Prestwick3_000140; Spectrum2_001329; Spectrum3_000565; Spectrum4_000352; Spectrum5_001112; DSSTox_CID_3645; EC 200-481-9; SCHEMBL3098; DSSTox_RID_77127; DSSTox_GSID_23645; BSPBio_000220; BSPBio_001950; KBioGR_000783; KBioSS_001514; BIDD:GT0653; DivK1c_000827; SCHEMBL537050; SPBio_001457; SPBio_002159; BPBio1_000242; SCHEMBL2116649; SCHEMBL2116661; DTXSID7023645; SCHEMBL21271987; GTPL10927; KBio1_000827; KBio2_001514; KBio2_004082; KBio2_006650; KBio3_001450; NINDS_000827; HMS2090B04; Tetracycline, >=98.0% (NT); HY-A0107; RKL10088; Tetracycline, >=88.0% (HPLC); Tox21_300150; BDBM50237605; s4490; ZINC84441937; AKOS024277860; AKOS026749977; ZINC100303069; ZINC102229720; CS-8188; DB00759; MCULE-3752961261; CAS-60-54-8; IDI1_000827; NCGC00017323-03; NCGC00017323-04; NCGC00017323-05; NCGC00017323-07; NCGC00017323-15; NCGC00142507-02; NCGC00254063-01; 4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,1 0,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide; BT166207; SBI-0051530.P003; 1369-EP2269978A2; 1369-EP2269985A2; 1369-EP2269991A2; 1369-EP2270008A1; 1369-EP2275420A1; 1369-EP2284150A2; 1369-EP2284151A2; 1369-EP2284152A2; 1369-EP2284153A2; 1369-EP2284155A2; 1369-EP2284156A2; 1369-EP2284164A2; 1369-EP2287140A2; 1369-EP2287148A2; 1369-EP2287150A2; 1369-EP2289871A1; 1369-EP2289891A2; 1369-EP2292088A1; 1369-EP2292590A2; 1369-EP2292612A2; 1369-EP2292617A1; 1369-EP2295402A2; 1369-EP2295419A2; 1369-EP2298732A1; 1369-EP2301534A1; 1369-EP2301912A2; 1369-EP2301913A1; 1369-EP2301914A1; 1369-EP2301916A2; 1369-EP2305637A2; 1369-EP2305640A2; 1369-EP2305662A1; 1369-EP2307027A1; 1369-EP2308832A1; 1369-EP2308863A1; 1369-EP2308883A1; 1369-EP2311451A1; 1369-EP2311796A1; 1369-EP2311797A1; 1369-EP2311798A1; 1369-EP2311799A1; 1369-EP2311822A1; 1369-EP2314583A1; 1369-EP2316450A1; 1369-EP2371797A1; 1369-EP2371798A1; 1369-EP2371800A1; 1369-EP2371804A1; C06570; D00201; AB00053550-04; AB00053550_05; AB00053550_06; Q193045; SR-01000000212-3; Z2144222809; (4S,4aS,5aS,6S,12aS)-2-[Amino(hydroxy)methylene]-4beta-(dimethylamino)-1,2,3,4,4a,5,5a,6,11,12a-decahydro-6alpha,10,12,12abeta-tetrahydroxy-6-methylnaphthacene-1,3,11-trione; (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-4,4a,5,5a-tetrahydrotetracene-2-carboxamide

Activity data
Interaction ID 782
Target type Molecule
Target unique ID 54675776
Activity 1 μM
Binding Conditions/Buffer

10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 250 mM NaCl
Assay

Photoinduced tetracycline crosslinking to the cb28 minimer. Reverse transcription of cb28 RNA, which was UV irradiated in the presence of increasing amounts of tetracycline. G and A indicate sequencing lanes
PubMed ID 11557342
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_171 RNA GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC 54.55%
Apta_256 RNA GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU 53.42%
Apta_224 RNA GGGGCCACCAACGACAUUGAACCACGUAGGCUCGUUUCUGAGCCGAUCUCGAUGUUGAUAUAAAUAGUGCCCAUGGAUC 51.90%
Apta_269 RNA AACGCUCAACGUCAGAAGGCAACGUAUAGGCAAGCACACUUCGACAUGAGGC 51.67%
Apta_424 RNA UGCUAGUAUAUCGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 51.67%
Apta_425 RNA UGCCGCCAUAUCACACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 51.67%
Apta_426 RNA UGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 51.67%
Apta_156 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU 51.35%
Apta_397 RNA GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_416 RNA GGACCUCGGCGAAAGCCGGUAACGCCACAAGUCGGAGGGUAAGAUCUGACAGGAACUGGGUGACGGAGGUUAGGUGC 50.65%
Apta_225 RNA GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC 50.63%
Apta_400 RNA GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA 50.63%
Apta_51 RNA GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC 50.00%
Apta_53 RNA UCCCUGGCCCAAGAUCCUAAUAAAGUUUUUUCGGACCGGAGCGAAACCACUAUCCUCUUAAGCAAUCUGU 50.00%
Apta_55 RNA GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC 50.00%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_303 RNA CCUCCGGCUCAUACCUUUUCGAAGACAAGCUUCGACAGGAGG 50.00%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_668 RNA GGAACCCAACUAGGCGUUUGAGGGGAUUCGGCCACGGUAACAACCCCUC 50.00%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
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