Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 771
Aptamer sequence: ATCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGA
Target unique ID: 161456
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_699 sgc8 Molecule Pyropheophorbide a N/A N/A 32584586
Structure information of aptamer
Aptamer Sequence: ATCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGA
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_699 Description sgc8
Aptamer chemistry DNA Length 41 nt
GC content 51.2% Molecular weight 12,634.13 Da
Molarity of 1 μg/μl solution 79.15 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence ATCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGA
Applications Fluorescence signal for tumor cell imaging and diagnosis; APCs efficiently penetrated into the interior of multicellular tumor spheroids (MCTS) and caused cell damage
Target information
Type Detail Type Detail
PubChem ID 161456 Molecular name Pyropheophorbide a
Molecular formula C33H34N4O3 Molecular weight 534.6
IUPAC name 3-[(21S,22S)-16-ethenyl-11-ethyl-4-hydroxy-12,17,21,26-tetramethyl-7,23,24,25-tetrazahexacyclo[18.2.1.15,8.110,13.115,18.02,6]hexacosa-1,4,6,8(26),9,11,13(25),14,16,18(24),19-undecaen-22-yl]propanoic acid InChIKey FDKRLXBXYZKWRZ-UWJYYQICSA-N
LogP 6.709 Topological polar surface area 106.64
Hydrogen bond acceptor 6 Hydrogen bond donor 3

Synonym(s):
Pyropheophorbide a; Pyropheophorbide-a; 24533-72-0; PYROPHEOPHORBIDE; CHEBI:48398; 3-[(21S,22S)-16-ethenyl-11-ethyl-4-hydroxy-12,17,21,26-tetramethyl-7,23,24,25-tetrazahexacyclo[18.2.1.15,8.110,13.115,18.02,6]hexacosa-1,4,6,8(26),9,11,13(25),14,16,18(24),19-undecaen-22-yl]propanoic acid; (3S-trans)-9-ethenyl-14-ethyl-4,8,13,18-tetramethyl-20-oxo-3-phorbinepropanoic acid; 3-[(3S,4S)-14-ethyl-4,8,13,18-tetramethyl-20-oxo-9-vinylphorbin-3-yl]propanoic acid; Pyropheophorbide alpha; PpaPpa; pyrophaeophorbide; SCHEMBL378992; CHEMBL520220; CHEMBL1807359; 3-Phorbinepropanoic acid, 9-ethenyl-14-ethyl-4,8,13,18-tetramethyl-20-oxo-, (3S,4S)-; 3-Phorbinepropanoic acid, 9-ethenyl-14-ethyl-4,8,13,18-tetramethyl-20-oxo-, (3S-trans)-; HY-128973; CS-0102957; C18064; J-015556; 3-(ethyl-tetramethyl-oxo-vinyl-[?]yl)propanoic acid; Q27121183; 7beta-(2-Carboxyethyl)-13-ethenyl-7,8-dihydro-2,8alpha,12,17-tetramethyl-18-ethyl-3,5-(carbonylmethylene)-21H,23H-porphyrin

Activity data

No relevant experimental diagram

 Interaction ID 771
Target type Molecule
Target unique ID 161456
Activity N/A
Binding Conditions/Buffer

N/A
Assay

N/A
PubMed ID 32584586

No relevant experimental diagram

 Interaction ID 889
Target type Cell
Target unique ID CRL-8199
Activity 0.78 nM
Binding Conditions/Buffer

0.1 mg/ml yeast tRNA and 1 mg/ml BSA into wash buffer (4.5g/L glucose, 5 mM MgCl2 in Dulbecco's PBS with CaCl2 and MgCl2)
Assay

N/A
PubMed ID 17373017
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1060 DNA AGCAATATTGCCCGCGCGGGGCCAACTGTCCTCACATGA 58.54%
Apta_1087 DNA CTTACGACTCAGGCATTTTGCCGGGTAACGAAGTTACTGTCGTAAG 54.35%
Apta_808 DNA GGGTCTTCCTGGACTGTCGAAAATTCAGTATCGGGAGG 53.66%
Apta_1149 DNA ATCATGGTGGGTATCGGCACTCGTTGGTTGAT 53.66%
Apta_750 DNA ATGCGAACAGGTGGGTGGGTTGGGTGGATTGTTCGGCTTCTTGAT 53.33%
Apta_1034 DNA ATGCGGATCCCGCGCGCGACCGTGTCAGCGGGGACTAGCGGTGTAGCGCGAAGCTTGCGC 51.67%
Apta_1230 DNA GGCGATAGGCAGTGTTGCGGGGTCGGAGAGCGAGGTAATAGCGTGTATGGGTGCTGTGTG 51.67%
Apta_65 DNA CTACCGTGGTAGGGAAGGTTGGAGTGTAG 51.22%
Apta_829 DNA CCCTCCGGGGGGGTCATCGGGATACCTGGTAAGGATA 51.22%
Apta_1013 DNA ATCACGTATGGGGGGCCGGCATGAGGGCCGCGCGTGACA 51.22%
Apta_1208 DNA CCCTGCGGGGCTGCCCGATATGTGTCCAGGTGGTG 51.22%
Apta_1262 DNA ACAAGGGGTGCAGGGGTCCGCGATTGTGACTGTGTGTGCG 51.22%
Apta_641 DNA TTCAAGACGATGCCTGGCGCGAGTTACACACTTGCATGGAGCTGG 51.11%
Apta_282 DNA ATCCATGGGGCGGAGATGAGGGGGAGGAGGGCGGGTACCCGGTTGAT 51.06%
Apta_421 DNA ATCTACGAATTCATCAGGGCTAAAGAGTGCAGAGTTACTTAGCCCGTGA 51.02%
Apta_621 DNA AAGCTTGCTTTATAGCCTGCAGCGATTCTTGATCGGAAAAGGCTGAGAGCTACGC 50.91%
Apta_279 DNA TTTTTTTTGGGCGAAGACCGGGACGGGAGGAAAGAGATGTTTGGTTTT 50.00%
Apta_523 DNA ATCCGTCACACCTGCTCTGACGCTGGGGTCGACCCGGAGAAATGCATTCCCCTGTGGTGTTGGCTCCCGTAT 50.00%
Apta_664 DNA CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA 50.00%
Apta_591 DNA CTCTCGGGACGACGGCTGGCACGTTTGGTTCAAGAATGTGGGTGTCGTCCC 49.02%

ABOUT

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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