Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 593
Aptamer sequence: GGAAGAGAUGGCGACUAAAACGACUUGUCGC
Target unique ID: 6076
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_560 Undefined Molecule Cyclic AMP 10 μM 20 mM Tris-HCl (pH 7.5 at 23 °C), 450 mM NaCl, 100 mM KCl, 10 mM MgCl2, 1 mM MnCl2, and 5 mM CaCl2 10913311
Structure information of aptamer
Aptamer Sequence: GGAAGAGAUGGCGACUAAAACGACUUGUCGC
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_560 Description Undefined
Aptamer chemistry RNA Length 31 nt
GC content 51.6% Molecular weight 10,044.07 Da
Molarity of 1 μg/μl solution 99.56 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence GGAAGAGAUGGCGACUAAAACGACUUGUCGC
Applications Recognition of cAMP
Target information
Type Detail Type Detail
PubChem ID 6076 Molecular name Cyclic AMP
Molecular formula C10H12N5O6P Molecular weight 329.21
IUPAC name (4aR,6R,7R,7aS)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol InChIKey IVOMOUWHDPKRLL-KQYNXXCUSA-N
LogP -0.817 Topological polar surface area 154.84
Hydrogen bond acceptor 10 Hydrogen bond donor 3

Synonym(s):
Cyclic AMP; cAMP; 60-92-4; Adenosine 3',5'-cyclic monophosphate; 3',5'-cyclic AMP; Adenosine 3',5'-cyclophosphate; Adenosine 3',5'-phosphate; Adenosine cyclophosphate; cyclic 3',5'-AMP; Adenosine cyclic monophosphate; cyclic 3',5'-Adenylic acid; Adenosine 3',5'-monophosphate; Adenosine-3',5'-cyclophosphate; cyclic Adenosine 3',5'-phosphate; Cyclic adenylic acid; 3',5'-AMP; Adenosine 3',5'-cyclic phosphate; cyclic Adenosine 3',5'-monophosphate; Adenosine cyclic 3',5'-monophosphate; Adenosine, cyclic 3',5'-(hydrogen phosphate); Adenosine cyclic 3',5'-phosphate; CCRIS 4291; Adenosine cyclic phosphate; [3H]cAMP; Cyclic Adenosine Monophosphate; [3H]-cAMP; UNII-E0399OZS9N; NSC 94017; Acrasin; adenosine-3',5'-cyclic-monophosphate; Adenosine 3',5'-phosphate monohydrate; BRN 0052645; CHEBI:17489; Adenosine cyclicphosphate; CHEMBL316966; E0399OZS9N; MFCD00005845; (4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)-2,7-dihydroxy-hexahydro-1,3,5,2$l^{5}-furo[3,2-d][1,3,2$l^{5}]dioxaphosphinin-2-one; (4aR,6R,7R,7aS)-6-(6-aminopurin-9-yl)-2-hydroxy-2-oxo-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol; NCGC00093588-03; Adenosine 3,5'-cyclic monophosphoric acid; DSSTox_CID_20436; DSSTox_RID_79492; DSSTox_GSID_40436; 114697-05-1; adenosine-cyclic-phosphate; 3',5'-cAMP; adenosine cyclic-monophosphate; adenosine-cyclic-phosphoric-acid; Siloxanes and Silicones, lauryl Me, Me hydrogen, Me 3-(oxiranylmethoxy)propyl, Me 2-phenylpropyl; EINECS 200-492-9; Adenosine-3',5'-cyclic phosphate; C10H12N5O6P; Adenosine 3'-,5'-cyclic monophosphate; CAS-60-92-4; 3'5'-cyclic AMP; CYCLIC AMP; CAMP; Cyclic 3',5'-adenylate; bmse000071; Epitope ID:137352; SCHEMBL1244; Adenosini Cycloghosghas,(S); Lopac0_000084; 4-26-00-03618 (Beilstein Handbook Reference); 3' 5'-adenosine monophosphate; GTPL2352; GTPL5096; cAMP; 3',5'-Cyclic AMP; DTXSID8040436; BDBM10851; cid_23902375; HMS3260A10; 6-(6-Amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide; HY-B1511; ZINC3873977; Tox21_113510; Tox21_500084; Adenosine-3',5'-cyclicmonophosphate; BDBM50384264; s9370; Adenosine 3',5'-cyclophosphoric acid; Adenosine 3':5'-cyclic monophosphate; Adenosine 3,5'-cyclic monophosphorate; AKOS015999561; Cyclic 3',5'-monophosphate adenosine; Tox21_113510_1; 3', 5'-cyclic adenosine monophosphate; adenosine 3',5'-(hydrogen phosphate); CCG-204179; DB02527; LP00084; SDCCGSBI-0050072.P002; Adenosine 3a(2),5a(2)-cyclophosphate; Adenosine-3',5'-cyclophosphate (cAMP); NCGC00093588-01; NCGC00093588-02; NCGC00093588-04; NCGC00093588-06; NCGC00260769-01; AS-13112; H355; Adenosine, 3',5'-cyclic-monophosphoric acid; CS-0013299; EU-0100084; Adenosine cyclic 3',5'-(hydrogen phosphate); ADENOSINE-3 ,5 -CYCLIC-MONOPHOSPHATE; A 9501; A51099; C00575; 005C845; Q210041; SR-01000075695; CYCLIC-3',5'-(HYDROGEN PHOSPHATE)ADENOSINE; SR-01000075695-1; 4H-Furo[3,2-d]-1,3,2-dioxaphosphorin, adenosine deriv.; Adenosine 3'',5''-cyclic phosphate (6CI); Cyclic 3'',5''-; B5C9F048-77DD-4170-A624-23C09E7B080D; Adenosine 3',5'-cyclic monophosphate, >=98.5% (HPLC), powder; Adenosine-3 inverted exclamation mark ,5 inverted exclamation mark -cyclic phosphoric acid; CAMP;Adenosine 3 inverted exclamation marka,5 inverted exclamation marka-cyclic monophosphat; (1S,6R,8R,9R)-8-(6-aminopurin-9-yl)-3-hydroxy-3-oxo-2,4,7-trioxa-3$l^{5}-phosphabicyclo[4.3.0]nonan-9-ol; (2R,4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide; (4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)-2,7-dihydroxy-hexahydro-1,3,5,2$l^{5}-furo[3,2-d][1,3,2]dioxaphosphinin-2-one; (4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide; (4aR,6R,7R,7aS)-6-(6-Aminopurin-9-yl)-2-oxo-tetrahydro-2-lambda*5*-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol; 4H-furo[3,2-d]-1,3,2-dioxaphosphorin-7-ol, 6-(6-amino-9H-purin-9-yl)tetrahydro-2-hydroxy-, 2-oxide, (4aR,6R,7R,7aS)-; 6-(6-Amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide #

Activity data
Interaction ID 593
Target type Molecule
Target unique ID 6076
Activity 10 μM
Binding Conditions/Buffer

20 mM Tris-HCl (pH 7.5 at 23 °C), 450 mM NaCl, 100 mM KCl, 10 mM MgCl2, 1 mM MnCl2, and 5 mM CaCl2
Assay

Determination of the KD for the aptamer ligand complex using equilibrium filtration
PubMed ID 10913311
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_371 RNA GGCAGACCAUACGGGAGAGAAACUUGCC 58.06%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 57.89%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 57.89%
Apta_230 RNA GGGAGGACGAUGCGGGCGUGAAUGGUGUUGUGAGG 57.14%
Apta_370 RNA GGGAGGACGCGUCGCCGUAAUGGAUGUUUUGCUCCCUG 55.26%
Apta_386 DNA GGAAAAGATGGTATGGGCCCTAGAAAGTCCACCCGGCGCC 55.00%
Apta_138 RNA GGAGGUGCUCCGAAAGGAACUCC 54.84%
Apta_241 RNA GCUUGACGGAGAUCAAGGGCGAGUCUCAUACCAAGUUGAUGGGG 54.55%
Apta_713 RNA GGCGGUGCUGGCCGAAAGGCGCUUGGAAACGUC 54.55%
Apta_86 RNA GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU 54.29%
Apta_1167 RNA GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC 52.78%
Apta_56 DNA GCAGCTAAGCAGGCGGCTCACAAAACCATTCGCATGCGGC 52.50%
Apta_367 RNA CGAGCGUAGAAUGUCUUCCCACUAGACGUCGUUCGGCCCC 52.50%
Apta_633 RNA GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC 52.50%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 51.61%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 51.61%
Apta_378 RNA UGCUCUUAGAAUGGGACUAAGACACGGGAC 51.61%
Apta_712 RNA GGCGGUGCUCGCCGAAAGGCUCCUGGAUACGUC 51.52%
Apta_94 RNA AUGACAGGAUGCAGAGCUCCACUGUCUAGUGUUUA 51.43%
Apta_388 RNA GCGGAAGCGUGCUGGGCUAGAAUAAUAAUAAGAAAACCAGUACUUUCGU 51.02%

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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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