{"ymdb_id":"YMDB00452","created_at":"2011-05-29T18:18:27.000Z","updated_at":"2016-09-08T18:35:29.000Z","name":"3',5'-cyclic dAMP","cas":"13342-50-2","state":null,"melting_point":null,"description":"Cyclic deoxyadenosine monophosphate (cdAMP) is a cyclic deoxyribonucleotide.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"28074","hmdb_id":null,"kegg_id":"C00968","pubchem_id":"188955","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"(4aR,6R,7aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-hexahydro-2λ⁵-furo[3,2-d][1,3,2]dioxaphosphinin-2-one","traditional_iupac":"3',5'-Cyclic dAMP","logp":"-2.908970341306835","pka":"18.53996070325955","alogps_solubility":"2.92e+00 g/l","alogps_logp":"-2.00","alogps_logs":"-2.03","acceptor_count":"7","donor_count":"2","rotatable_bond_count":"1","polar_surface_area":"134.61","refractivity":"68.7788","polarizability":"27.83042554894695","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"5.001510161284282","pka_strongest_acidic":"1.857516571801571","bioavailability":"1","number_of_rings":"4","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2'-deoxy cyclic AMP","2'-deoxyadenosine cyclic 3',5'-(hydrogen phosphate)","3',5'-Cyclic dAMP","3',5'-cyclic deoxyadenylic acid","3',5'-cyclic-2'-dAMP"],"pathways":[],"growth_conditions":[],"references":[{"pubmed_id":18846089,"citation":"Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). \"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.\" Nat Biotechnol 26:1155-1160."},{"pubmed_id":18135,"citation":"Londesborough, J. (1977). \"Characterization of an adenosine 3':5'-cyclic monophosphate phosphodiesterase from baker's yeast. Its binding to subcellular particles, catalytic properties and gel-filtration behaviour.\" Biochem J 163:467-476."}],"proteins":[{"created_at":"2011-05-26T19:20:47.000Z","updated_at":"2011-07-22T17:53:44.000Z","name":"3',5'-cyclic-nucleotide phosphodiesterase 2","uniprot_id":"P06776","uniprot_name":"PDE2_YEAST","enzyme":true,"transporter":false,"gene_name":"PDE2","num_residues":526,"molecular_weight":"60999.19922","theoretical_pi":"6.6","general_function":"Involved in catalytic activity","specific_function":"Controls the level of cAMP in yeast cells, together with the low-affinity cAMP phosphodiesterase (PDE1)","reactions":[{"id":1155,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1156,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1157,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1158,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1159,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2564,"direction":"\u003e","locations":"Cytoplasmic","altext":"Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 5'-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"M14563","genbank_protein_id":"172106","gene_card_id":"PDE2","chromosome_location":"chromosome 15","locus":"YOR360C","synonyms":["PDEase 2","High-affinity cAMP phosphodiesterase"],"enzyme_classes":["3.1.4.17"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on ester bonds"},{"category":"Function","description":" phosphoric ester hydrolase activity"},{"category":"Function","description":" phosphoric diester hydrolase activity"},{"category":"Function","description":" cyclic-nucleotide phosphodiesterase activity"},{"category":"Function","description":" 3',5'-cyclic-nucleotide phosphodiesterase activity"},{"category":"Process","description":" biological regulation"},{"category":"Process","description":" regulation of biological process"},{"category":"Process","description":" regulation of cellular process"},{"category":"Process","description":" signal transduction"}],"pfams":[{"name":"PDEase_I","identifier":"PF00233"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"gene_sequence":"ATGTCCACCCTTTTTCTGATTGGAATACACGAGATTGAGAAATCTCAAACAATTGTACAGAATGAACACTATTTTGATAGAGTGATTGAGCTTCAAGATTTGGATTCTCTGATGGTAGCATTGTATAAGGACAGAGTTTCGCCTTTTCCAAACGTCCATAACTTTGAAACGGGCGTATCTATAGTTCTTTATGACCCTTCAAAATTTCAATTATCTGTGCGACAATTGGATGTTCTATTCAAGGGATTTTTCCCATCTTTCAATATTTCTGCGATAGATCATACACGAGAGGAAAACCTGCAACGTCTGGAATGTGTTGAGCGTGAAAATAGCATCTGTCGTAATAGAATAACGAGAATTAACCACTGGATGTATCACCATCATGATGATACTCCAGACGGTATTAACAAAAACAGCTATGGTACTGTAAATGGGAATTCTGTCCCCACTCAAGCATGTGAAGCAAACATTTACACTTTATTATTGCATTTGAATGATTCCAAGGCACAACATTTACGAAAGGCATCAGTGCCAAGGCTAATTCGCAACATCGAGTTTATGTCTTTTTTGTCAGATCCAATAGAAAAAATTTCTCAAGAGGGATCACATTATTGGAACATTCTATCAACTTGGGACTTTTGTGCTTTATCATTAAGCACTCAAGAATTGATTTGGTGCGGGTTCACGCTTATCAAAAAATTATCTAAGGATGCAAAAGTACTCATTGCAGATAATAAGTTACTGCTACTACTATTTACTTTAGAATCATCCTATCATCAAGTTAACAAATTTCACAATTTTAGGCATGCCATCGATGTCATGCAAGCCACATGGCGATTGTGTACATATCTTCTTAAAGATAATCCTGTACAAACATTACTGTTGTGTATGGCTGCCATAGGTCATGATGTCGGTCATCCTGGGACTAACAATCAACTATTGTGCAACTGTGAATCAGAGGTTGCTCAAAATTTCAAAAATGTCTCTATCTTGGAGAATTTTCACAGGGAATTATTTCAACAATTGCTATCAGAGCATTGGCCTCTTAAGCTCTCTATCTCCAAAAAAAAATTTGATTTTATTTCCGAGGCTATTCTGGCCACAGATATGGCATTGCATTCTCAGTATGAGGATAGATTAATGCATGAAAACCCAATGAAACAAATCACTTTGATATCTCTAATTATTAAAGCTGCAGACATCTCTAATGTGACGAGAACCTTGTCAATATCAGCACGTTGGGCATACCTCATTACTCTCGAATTTAATGATTGCGCTCTTTTGGAAACATTTCATAAAGCTCACCGCCCAGAACAAGACTGTTTTGGCGATTCATACAAGAATGTTGATTCTCCGAAAGAAGATTTGGAATCAATTCAAAATATTTTGGTGAACGTAACAGACCCTGATGATATTATCAAAGACCATCCGCATATTCCAAACGGTCAAATATTTTTCATTAATACGTTTGCTGAAGTATTTTTCAACGCATTAAGTCAAAAATTCTCAGGATTAAAATTTTTAAGCGATAATGTCAAAATCAATAAAGAATACTGGATGAAACACAAGAAACCACAATAG","protein_sequence":"MSTLFLIGIHEIEKSQTIVQNEHYFDRVIELQDLDSLMVALYKDRVSPFPNVHNFETGVSIVLYDPSKFQLSVRQLDVLFKRFFPSFNISAIDHTREENLQRLECVERENSICRNRITRINHWMYHHHDDTPDGINKNSYGTVNGNSVPTQACEANIYTLLLHLNDSKAQHLRKASVPRLIRNIEFMSFLSDPIEKISQEGSHYWNILSTWDFCALSLSTQELIWCGFTLIKKLSKDAKVLIADNKLLLLLFTLESSYHQVNKFHNFRHAIDVMQATWRLCTYLLKDNPVQTLLLCMAAIGHDVGHPGTNNQLLCNCESEVAQNFKNVSILENFHRELFQQLLSEHWPQLLSISKKKFDFISEAILATDMALHSQYEDRLMHENPMKQITLISLIIKAADISNVTRTLSISARWAYLITLEFNDCALLETFHKAHRPEQDCFGDSYKNVDSPKEDLESIQNILVNVTDPDDIIKDHPHIPNGQIFFINTFAEVFFNALSQKFSGLKFLSDNVKINKEYWMKHKKPQ"}]}