{"ymdb_id":"YMDB00503","created_at":"2011-05-29T18:24:24.000Z","updated_at":"2016-09-08T18:35:33.000Z","name":"2'-Deoxyadenosine","cas":"\r","state":"Solid","melting_point":null,"description":"2'-Deoxyadenosine (deoxyadenosine) is a purine deoxynucleoside. It is formed by a molecule of adenine attached to a deoxyribose sugar molecule. Deoxyadenosine is the DNA deoxynucleoside A.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"-0.55 [HANSCH,C ET AL. (1995)]","location":"extracellular;cytoplasm","synthesis_reference":"Munch-Petersen, Agnete.  Formation in vitro of deoxyadenosine triphosphate from deoxyadenosine in Ehrlich ascites cells.    Biochemical and Biophysical Research Communications  (1960),  3  392-6.","chebi_id":"17256","hmdb_id":"HMDB00101","kegg_id":"C00131","pubchem_id":"22209663","cs_id":"24765642","foodb_id":null,"wikipedia_link":"Deoxyadenosine","biocyc_id":"DEOXYADENOSINE","iupac":"(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol","traditional_iupac":"2-deoxyadenosine","logp":"-1.1903258086666668","pka":"14.785037392135134","alogps_solubility":"1.07e+01 g/l","alogps_logp":"-0.95","alogps_logs":"-1.37","acceptor_count":"7","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"119.30999999999999","refractivity":"61.68489999999999","polarizability":"24.236037685868787","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"3.9409008296129784","pka_strongest_acidic":"13.886733808608756","bioavailability":"1","number_of_rings":"3","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol","2-Deoxyadenosine","2-deoxyadenosine 5-triphosphate","2'-Deoxy-5'-ATP","2'-Deoxy-ATP","2'-Deoxyadenosine","2'-Deoxyadenosine 5'-triphosphate","2'-deoxyadenosine triphosphate","5-(6-AMINO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL","9-(2-Deoxy-beta-D-erythro-pentofuranosyl)adenine","9-(2-deoxy-beta-D-ribofuranosyl)-9H-purin-6-amine","9H-Purin-6-amine, 9-(2-deoxy-beta-D-ribofuranosyl)-","Adenine deoxy nucleoside","Adenine deoxyribonucleoside","Adenosine, 2'-deoxy-","Adenyldeoxyriboside","beta-D-Erythro-Pentofuranoside, adenine-9 2-deoxy-","beta-D-Ribofuranose, 1-(6-amino-9H-purin-9-yl)-1,2-dideoxy-","dA","dATP","Deoxy-ATP","Deoxyadenosine","deoxyadenosine 5-triphosphate","Deoxyadenosine 5'-triphosphate","deoxyadenosine triphosphate","deoxyadenosine-triphosphate","Desoxyadenosine","DTP"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Lipoic acid metabolism","kegg_map_id":"00785"},{"name":"purine nucleotides de novo biosynthesis","kegg_map_id":null}],"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":19889834,"citation":"Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). \"Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.\" Mol Biol Cell 21:198-211."}],"proteins":[{"created_at":"2011-05-24T20:49:32.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Purine nucleoside phosphorylase","uniprot_id":"Q05788","uniprot_name":"PNPH_YEAST","enzyme":true,"transporter":false,"gene_name":"PNP1","num_residues":311,"molecular_weight":"33754.60156","theoretical_pi":"7.31","general_function":"Involved in purine-nucleoside phosphorylase activity","specific_function":"Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules","reactions":[{"id":1447,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1915,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1916,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1917,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1918,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1919,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1920,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1921,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2012,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2349,"direction":"\u003e","locations":null,"altext":"Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY557950","genbank_protein_id":"45269792","gene_card_id":"PNP1","chromosome_location":"chromosome 12","locus":"YLR209C","synonyms":["PNP","Inosine phosphorylase"],"enzyme_classes":["2.4.2.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Function","description":" purine-nucleoside phosphorylase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside metabolic process"}],"pfams":[{"name":"PNP_UDP_1","identifier":"PF01048"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"Nicotinate and nicotinamide metabolism","kegg_map_id":"00760"}],"gene_sequence":"ATGAGTGATATCTTGAACGTAAGTCAACAACGTGAAGCAATTACCAAGGCCGCTGCGTATATTTCTGCTATTTTAGAACCACATTTCAAAAATACAACAAATTTCGAGCCTCCGAGAACTTTGATTATATGTGGTTCAGGGCTTGGTGGAATATCTACCAAGCTGTCTAGAGACAATCCACCCCCGGTAACAGTCCCATACCAAGACATCCCAGGATTCAAGAAAAGTACGGTTCCAGGTCATTCCGGTACACTAATGTTCGGATCTATGAATGGTTCACCAGTAGTATTAATGAATGGTCGTCTTCATGGATATGAAGGCAACACATTGTTTGAGACTACTTTTCCTATTAGAGTGCTTAACCACATGGGTCATGTTCGTAATTTAATTGTCACTAATGCCGCTGGTGGTATAAACGCGAAATATCAAGCCTGCGATTTGATGTGCATTTATGATCATTTAAATATCCCTGGCCTTGCTGGCCAGCACCCATTGAGAGGTCCTAACTTGGATGAAGATGGACCTCGTTTTTTAGCCTTGAGTGATGCATATGATCTGGAGTTGAGGAAGCTTTTATTTAAGAAATGGAAAGAGCTCAAGATTCAAAGGCCACTGCATGAAGGTACTTATACTTTTGTATCTGGACCCACTTTCGAAACAAGAGCAGAATCCAAAATGATAAGGATGTTGGGAGGAGATGCTGTCGGAATGAGTACTGTTCCCGAAGTCATTGTTGCAAGACATTGCGGATGGAGGGTTTTGGCCTTAAGTTTGATTACCAATACTTGCGTGGTGGATAGCCCTGCCAGTGCGTTGGACGAATCACCTGTACCCTTAGAAAAAGGCAAAGCGACTCACGCTGAAGTACTGGAGAATGGTAAAATCGCCTCTAATGACGTGCAAAACTTAATTGCTGCCGTAATGGGGGAATTATAA","protein_sequence":"MSDILNVSQQREAITKAAAYISAILEPHFKNTTNFEPPRTLIICGSGLGGISTKLSRDNPPPVTVPYQDIPGFKKSTVPGHSGTLMFGSMNGSPVVLMNGRLHGYEGNTLFETTFPIRVLNHMGHVRNLIVTNAAGGINAKYQACDLMCIYDHLNIPGLAGQHPLRGPNLDEDGPRFLALSDAYDLELRKLLFKKWKELKIQRPLHEGTYTFVSGPTFETRAESKMIRMLGGDAVGMSTVPEVIVARHCGWRVLALSLITNTCVVDSPASALDESPVPLEKGKATHAEVLENGKIASNDVQNLIAAVMGEL"},{"created_at":"2011-05-26T16:49:15.000Z","updated_at":"2011-07-22T17:54:35.000Z","name":"Adenosine deaminase","uniprot_id":"P53909","uniprot_name":"ADA_YEAST","enzyme":true,"transporter":false,"gene_name":"AAH1","num_residues":347,"molecular_weight":"39634.69922","theoretical_pi":"5.07","general_function":"Involved in deaminase activity","specific_function":"Adenosine + H(2)O = inosine + NH(3)","reactions":[{"id":1266,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1268,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1440,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2446,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"Adenosine + H(2)O = inosine + NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"Z46843","genbank_protein_id":"854497","gene_card_id":"AAH1","chromosome_location":"chromosome 14","locus":"YNL141W","synonyms":["Adenosine aminohydrolase"],"enzyme_classes":["3.5.4.4","3.5.4.2"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" deaminase activity"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" adenosine deaminase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" purine nucleoside monophosphate biosynthetic process"},{"category":"Process","description":" purine ribonucleoside monophosphate biosynthetic process"}],"pfams":[{"name":"A_deaminase","identifier":"PF00962"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"gene_sequence":"ATGGTTTCTGTGGAGTTTTTACAGGAGTTACCAAAATGTGAGCATCACTTGCATTTGGAAGGTACTCTAGAACCTGACCTATTGTTCCCATTAGCTAAAAGAAACGATATAATTCTACCTGAAGGTTTTCCTAAATCGGTCGAGGAATTAAACGAAAAGTATAAGAAGTTTCGTGATCTGCAGGATTTCTTAGATTACTATTATATTGGTACTAATGTCTTGATTAGTGAACAAGATTTCTTTGATTTGGCGTGGGCCTATTTTAAAAAAGTTCACAAACAAGGCTTGGTCCATGCTGAAGTGTTTTACGACCCTCAGTCACATACATCTAGGGGCATCTCCATAGAAACAGTCACTAAAGGTTTCCAAAGAGCTTGTGACAAAGCCTTCTCTGAATTTGGTATTACATCCAAGCTAATTATGTGTCTGTTAAGACACATTGAACCAGAGGAATGTTTGAAAACTATCGAAGAAGCTACCCCATTTATTAAAGATGGTACTATCTCTGCCTTAGGATTAGATTCTGCTGAGAAACCATTTCCCCCACATTTATTTGTTGAATGTTACGGAAAGGCCGCCTCATTGAATAAAGATTTAAAACTAACTGCACACGCAGGTGAAGAAGGCCCCGCTCAATTCGTCTCGGATGCTTTAGACTTGTTGCAAGTAACAAGAATCGATCACGGTATCAACAGTCAATACGACGAGGAGTTATTGGATAGGTTGTCGCGCGACCAGACCATGCTAACTATTTGTCCTCTCTCCAACGTGAAGCTACAAGTAGTCCAATCCGTTTCAGAGTTACCACTACAAAAGTTTCTTGACAGAGATGTTCCATTTTCTTTAAATTCTGATGACCCCGCCTATTTTGGTGGTTATATCTTAGATGTCTACACTCAAGTTTCGAAAGATTTCCCACACTGGGACCATGAAACATGGGGTCGTATCGCTAAGAACGCCATTAAAGGTTCATGGTGTGACGATAAAAGAAAGAACGGTTTGTTAAGTAGAGTGGACGAAGTAGTCACTAAATATTCGCATTAG","protein_sequence":"MVSVEFLQELPKCEHHLHLEGTLEPDLLFPLAKRNDIILPEGFPKSVEELNEKYKKFRDLQDFLDYYYIGTNVLISEQDFFDLAWAYFKKVHKQGLVHAEVFYDPQSHTSRGISIETVTKGFQRACDKAFSEFGITSKLIMCLLRHIEPEECLKTIEEATPFIKDGTISALGLDSAEKPFPPHLFVECYGKAASLNKDLKLTAHAGEEGPAQFVSDALDLLQVTRIDHGINSQYDEELLDRLSRDQTMLTICPLSNVKLQVVQSVSELPLQKFLDRDVPFSLNSDDPAYFGGYILDVYTQVSKDFPHWDHETWGRIAKNAIKGSWCDDKRKNGLLSRVDEVVTKYSH"},{"created_at":"2011-05-27T02:12:57.000Z","updated_at":"2011-05-27T15:01:17.000Z","name":"Lipoyl synthase, mitochondrial","uniprot_id":"P32875","uniprot_name":"LIPA_YEAST","enzyme":true,"transporter":false,"gene_name":"LIP5","num_residues":414,"molecular_weight":"46246.80078","theoretical_pi":"10.05","general_function":"Involved in catalytic activity","specific_function":"Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives (Probable)","reactions":[{"id":2662,"direction":"\u003e","locations":"Mitochondrion","altext":"Protein N(6)-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine = protein N(6)-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosine.","export":false,"pw_reaction_id":null,"source":null},{"id":14866,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007053","source":"Smpdb"},{"id":14867,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007054","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"AY558046","genbank_protein_id":"45269982","gene_card_id":"LIP5","chromosome_location":"chromosome 15","locus":"YOR196C","synonyms":["Lipoate synthase","LS","Lip-syn","Lipoic acid synthase"],"enzyme_classes":["2.8.1.8"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" metal cluster binding"},{"category":"Function","description":" iron-sulfur cluster binding"},{"category":"Function","description":" 4 iron, 4 sulfur cluster binding"},{"category":"Function","description":" transferase activity, transferring sulfur-containing groups"},{"category":"Function","description":" sulfurtransferase activity"},{"category":"Function","description":" lipoate synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cofactor metabolic process"},{"category":"Process","description":" coenzyme metabolic process"},{"category":"Process","description":" lipoic acid metabolic process"},{"category":"Process","description":" lipoic acid biosynthetic process"},{"category":"Process","description":" lipoate biosynthetic process"}],"pfams":[{"name":"Radical_SAM","identifier":"PF04055"}],"pathways":[{"name":"Lipoic acid metabolism","kegg_map_id":"00785"}],"gene_sequence":"ATGTATAGACGATCTGTTGGAGTACTATTTGTTGGGAGAAATACAAGATGGATTTCGTCCACTATTAGGTGTGGAACGAGCGCAACTCGGCCAATAAGATCCAATGCATTGAATACTGATTCAGATAACGCTAGCGTTAGGGTACCAGTTGGAAATTCAACTGAGGTTGAAAATGCAACCAGTCAGTTAACAGGGACTTCGGGAAAAAGACGCAAGGGGAACAGAAAAAGAATTACAGAGTTCAAAGATGCTCTTAATTTGGGTCCATCTTTTGCAGATTTTGTTTCAGGTAAAGCTTCGAAAATGATCTTGGACCCTCTGGAGAAGGCAAGGCAAAATACAGAGGAAGCTAAAAAACTACCTCGTTGGCTTAAGGTTCCTATTCCTAAGGGTACCAATTACCATAAATTGAAAGGCGACGTAAAAGAATTAGGCCTGAGTACTGTTTGTGAGGAGGCAAGATGTCCCAATATTGGTGAATGTTGGGGAGGCAAAGATAAATCTAAGGCAACGGCAACAATTATGCTGCTTGGTGATACTTGCACTCGTGGATGTAGGTTTTGTTCTGTGAAGACCAATAGAACGCCTAGTAAGCCGGACCCAATGGAGCCCGAAAATACTGCCGAAGCTATCAAAAGATGGGGGTTGGGTTATGTTGTTTTAACTACCGTTGATAGGGACGATTTAGTCGATGGTGGTGCTAATCACCTGGCCGAGACGGTTCGCAAAATCAAACAGAAGGCACCAAATACTCTTGTAGAGACTCTTTCTGGTGATTTCAGAGGTGATTTGAAGATGGTGGACATTATGGCACAATGTGGGCTTGATGTTTACGCACATAATTTGGAAACAGTTGAATCACTAACACCACATGTCAGAGACAGAAGAGCTACTTATAGACAGTCTTTGAGTGTTTTAGAAAGGGCAAAAGCTACGGTTCCGTCACTGATTACTAAAACATCAATAATGCTGGGTCTAGGAGAAACTGATGAGCAAATTACTCAAACTTTGAAGGATTTGCGCAATATTCAATGTGATGTTGTTACATTTGGTCAATATATGAGGCCAACCAAGAGACATATGAAAGTCGTAGAATATGTGAAACCCGAAAAGTTTGACTACTGGAAAGAGAGAGCTTTAGAGATGGGATTCTTGTATTGTGCATCTGGACCCCTAGTAAGATCGTCATATAAGGCTGGTGAAGCATTTATTGAGAACGTTTTGAAGAAAAGAAACATGAAATAA","protein_sequence":"MYRRSVGVLFVGRNTRWISSTIRCGTSATRPIRSNALNTDSDNASVRVPVGNSTEVENATSQLTGTSGKRRKGNRKRITEFKDALNLGPSFADFVSGKASKMILDPLEKARQNTEEAKKLPRWLKVPIPKGTNYHKLKGDVKELGLSTVCEEARCPNIGECWGGKDKSKATATIMLLGDTCTRGCRFCSVKTNRTPSKPDPMEPENTAEAIKRWGLGYVVLTTVDRDDLVDGGANHLAETVRKIKQKAPNTLVETLSGDFRGDLKMVDIMAQCGLDVYAHNLETVESLTPHVRDRRATYRQSLSVLERAKATVPSLITKTSIMLGLGETDEQITQTLKDLRNIQCDVVTFGQYMRPTKRHMKVVEYVKPEKFDYWKERALEMGFLYCASGPLVRSSYKAGEAFIENVLKKRNMK"}]}