{"ymdb_id":"YMDB00451","created_at":"2011-05-29T18:18:21.000Z","updated_at":"2016-09-08T18:35:29.000Z","name":"dAMP","cas":"653-63-4","state":"Solid","melting_point":"148 oC","description":"Deoxyadenosine monophosphate (dAMP) is a deoxyribonucleotide found in DNA. dAMP consists of a phosphate group, the sugar deoxy-ribose, and the nucleobase adenine. When found in DNA the adenosine portion of dAMP pairs with thymine protion of dTMP.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"mitochondrion;cytoplasm","synthesis_reference":"Scarano, E.  Incorporation of adenine-C14 into deoxyadenylic acid.    Bollettino - Societa Italiana di Biologia Sperimentale  (1958),  34  1620-1. ","chebi_id":"17713","hmdb_id":"HMDB00905","kegg_id":"C00360","pubchem_id":"621","cs_id":"25056912","foodb_id":null,"wikipedia_link":"Deoxyadenosine_monophosphate","biocyc_id":"DAMP","iupac":"{[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"DAMP","logp":"-3.847898303907523","pka":"6.2598694502185745","alogps_solubility":"2.71e+00 g/l","alogps_logp":"-2.44","alogps_logs":"-2.09","acceptor_count":"9","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"165.83999999999997","refractivity":"72.5578","polarizability":"28.980183076216395","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"3.9396602503688625","pka_strongest_acidic":"1.231362812852561","bioavailability":"1","number_of_rings":"3","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(3-Hydroxyphenyl)dimethylamine","2-deoxyadenosine 5-monophosphate","2-deoxyadenosine 5-phosphate","2'-dAMP","2'-deoxy-5'-adenosine monophosphate","2'-Deoxy-5'-adenylate","2'-Deoxy-5'-adenylic acid","2'-deoxy-Adenosine 5'-phosphorate","2'-deoxy-Adenosine 5'-phosphoric acid","2'-Deoxy-AMP","2'-deoxyadenosine 5'-(dihydrogen phosphate)","2'-Deoxyadenosine 5'-monophosphate","2'-Deoxyadenosine 5'-phosphate","2'-Deoxyadenosine monophosphate","2'-deoxyadenosine-5'-monophosphate","2'-deoxyadenosine-5'-phosphate","2'-Deoxyadenylate","2'-Deoxyadenylic acid","3-(Dimethylamino)phenol","3-Hydroxy-N,N-dimethylaniline","5'-Adenylic acid, 2'-deoxy-","Adenosine, 2'-deoxy-, 5'-(dihydrogen phosphate)","Adenosine, 2'-deoxy-, 5'-phosphoric acid","dAMP","Deoxy-5'-adenylate","Deoxy-5'-adenylic acid","Deoxy-AMP","Deoxyadenosine 5'-monophosphate","Deoxyadenosine 5'-phosphate","deoxyadenosine monophosphate","deoxyadenosine-phosphate","Deoxyadenylate","deoxyadenylic acid","m-(Dimethylamino)phenol","N,N-Dimethyl-m-aminophenol","PdA","PdA (VAN)","Phenol, m-(dimethylamino)-"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"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":17517786,"citation":"Gu, C., Wang, Y. (2007). \"In vitro replication and thermodynamic studies of methylation and oxidation modifications of 6-thioguanine.\" Nucleic Acids Res 35:3693-3704."},{"pubmed_id":19386622,"citation":"Ungar, L., Yosef, N., Sela, Y., Sharan, R., Ruppin, E., Kupiec, M. (2009). \"A genome-wide screen for essential yeast genes that affect telomere length maintenance.\" Nucleic Acids Res 37:3840-3849."},{"pubmed_id":18687109,"citation":"Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). \"The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.\" BMC Syst Biol 2:71."}],"proteins":[{"created_at":"2011-05-26T19:13:38.000Z","updated_at":"2011-05-26T19:13:38.000Z","name":"Uncharacterized mitochondrial carrier YIL006W","uniprot_id":"P40556","uniprot_name":"YIA6_YEAST","enzyme":false,"transporter":true,"gene_name":null,"num_residues":373,"molecular_weight":"41954.0","theoretical_pi":"8.83","general_function":"Involved in binding","specific_function":null,"reactions":[],"signal_regions":"None","transmembrane_regions":"81-101;142-162;177-199;236-256;281-297;336-358","pdb_id":null,"cellular_location":"Mitochondrion inner membrane; Multi-pass membrane protein","genbank_gene_id":"Z38113","genbank_protein_id":"558398","gene_card_id":null,"chromosome_location":null,"locus":"YIL006W","synonyms":[],"enzyme_classes":[],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" membrane"},{"category":"Component","description":" organelle membrane"},{"category":"Component","description":" organelle inner membrane"},{"category":"Component","description":" mitochondrial inner membrane"},{"category":"Function","description":" binding"},{"category":"Function","description":" transporter activity"},{"category":"Process","description":" transmembrane transport"},{"category":"Process","description":" establishment of localization"},{"category":"Process","description":" transport"}],"pfams":[{"name":"Mito_carr","identifier":"PF00153"}],"pathways":[],"gene_sequence":"ATGACACAGACTGATAATCCTGTCCCCAACTGCGGTTTACTGCCCGAGCAGCAGTATTGCTCTGCAGACCATGAAGAGCCACTGTTGTTGCATGAAGAACAATTGATATTCCCTGATCATTCCTCCCAACTGTCCTCAGCAGATATCATCGAGCCCATCAAGATGAACAGCAGTACTGAGTCAATTATAGGGACAACGCTGCGAAAGAAATGGGTACCACTATCCTCAACTCAGATCACAGCTCTTTCCGGCGCATTTGCTGGATTCTTATCAGGTGTGGCAGTATGTCCCCTCGATGTTGCCAAAACGCGATTGCAAGCACAAGGACTACAAACTAGGTTCGAGAACCCCTACTATAGGGGGATAATGGGGACATTAAGTACTATAGTAAGAGACGAAGGCCCGCGGGGCCTCTACAAAGGGCTGGTACCGATTGTCCTGGGCTACTTCCCAACCTGGATGATATACTTCTCCGTGTATGAATTCAGCAAAAAGTTCTTTCACGGCATCTTCCCACAGTTTGATTTTGTTGCTCAGTCATGTGCTGCAATCACGGCAGGCGCTGCATCTACCACCTTGACCAACCCAATCTGGGTTGTGAAGACAAGACTTATGCTGCAATCAAACCTCGGTGAGCACCCCACACATTACAAAGGCACTTTCGATGCATTCAGAAAGCTATTTTATCAGGAAGGGTTTAAAGCATTATATGCGGGGCTGGTCCCCTCATTATTAGGGCTATTTCATGTGGCTATCCATTTCCCTATATACGAAGATTTGAAGGTAAGATTTCACTGCTATTCTCGGGAGAACAACACCAACTCCATCAACTTGCAACGGTTGATCATGGCATCGTCCGTCTCTAAGATGATTGCATCAGCAGTAACATATCCGCACGAAATTTTACGAACCAGAATGCAACTGAAATCAGATATACCAGATTCCATTCAACGACGTCTGTTCCCCCTCATTAAAGCAACTTATGCACAAGAGGGACTAAAGGGATTTTATTCTGGATTTACTACTAACCTAGTACGAACCATTCCGGCCTCGGCAATCACTCTAGTGTCCTTTGAGTATTTCAGAAACCGCCTAGAAAATATTAGCACTATGGTAATTTAA","protein_sequence":"MTQTDNPVPNCGLLPEQQYCSADHEEPLLLHEEQLIFPDHSSQLSSADIIEPIKMNSSTESIIGTTLRKKWVPLSSTQITALSGAFAGFLSGVAVCPLDVAKTRLQAQGLQTRFENPYYRGIMGTLSTIVRDEGPRGLYKGLVPIVLGYFPTWMIYFSVYEFSKKFFHGIFPQFDFVAQSCAAITAGAASTTLTNPIWVVKTRLMLQSNLGEHPTHYKGTFDAFRKLFYQEGFKALYAGLVPSLLGLFHVAIHFPIYEDLKVRFHCYSRENNTNSINLQRLIMASSVSKMIASAVTYPHEILRTRMQLKSDIPDSIQRRLFPLIKATYAQEGLKGFYSGFTTNLVRTIPASAITLVSFEYFRNRLENISTMVI"},{"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":" cyclic-nucleotide phosphodiesterase activity"},{"category":"Function","description":" 3',5'-cyclic-nucleotide phosphodiesterase activity"},{"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":"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"}]}