{"ymdb_id":"YMDB00150","created_at":"2011-05-29T16:01:46.000Z","updated_at":"2016-09-08T18:35:06.000Z","name":"5'-Deoxyadenosine","cas":"4754-39-6","state":"Solid","melting_point":"213.0-214.5 oC","description":"Deoxyadenosine is a deoxyribonucleoside. It is a derivative of the nucleoside adenosine, differing from the latter by the replacement of a hydroxyl group (-OH) by hydrogen (-H) at the 2' position of its ribose sugar moiety. Deoxyadenosine is the DNA nucleoside A, which pairs with deoxythymidine (T) in double-stranded DNA. [Wikipedia]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"Cytoplasm, Extracellular","synthesis_reference":"Lerner, Leon M. An improved preparation of 5'-deoxyadenosine by coupling methods. Carbohydrate Research (1988), 184 250-3.","chebi_id":"17319","hmdb_id":"HMDB01983","kegg_id":"C05198","pubchem_id":"439182","cs_id":"388325","foodb_id":null,"wikipedia_link":"Deoxyadenosine","biocyc_id":"CH33ADO","iupac":"(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-methyloxolane-3,4-diol","traditional_iupac":"5'-deoxyadenosine","logp":"-1.0440539050000002","pka":"14.04065367928522","alogps_solubility":"9.88e+00 g/l","alogps_logp":"-0.52","alogps_logs":"-1.41","acceptor_count":"7","donor_count":"3","rotatable_bond_count":"1","polar_surface_area":"119.30999999999999","refractivity":"61.6519","polarizability":"24.30241412668001","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"3.9212963575149358","pka_strongest_acidic":"12.482511642166756","bioavailability":"1","number_of_rings":"3","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5'-deoxy-adenosine"],"pathways":[{"name":"Biotin Biosynthesis","kegg_map_id":null}],"growth_conditions":[],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."}],"proteins":[{"created_at":"2011-05-26T17:19:36.000Z","updated_at":"2011-07-22T17:54:19.000Z","name":"Biotin synthase, mitochondrial","uniprot_id":"P32451","uniprot_name":"BIOB_YEAST","enzyme":true,"transporter":false,"gene_name":"BIO2","num_residues":375,"molecular_weight":"41883.80078","theoretical_pi":"8.66","general_function":"Involved in catalytic activity","specific_function":"Dethiobiotin + sulfur + 2 S-adenosyl-L- methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine","reactions":[{"id":1347,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2472,"direction":"\u003e","locations":"Mitochondrion","altext":"Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine.","export":false,"pw_reaction_id":null,"source":null},{"id":3756,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006280","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"Z73071","genbank_protein_id":"1323523","gene_card_id":"BIO2","chromosome_location":"chromosome 7","locus":"YGR286C","synonyms":[],"enzyme_classes":["2.8.1.6"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" metal cluster binding"},{"category":"Function","description":" iron-sulfur cluster binding"},{"category":"Function","description":" transferase activity, transferring sulfur-containing groups"},{"category":"Function","description":" sulfurtransferase activity"},{"category":"Function","description":" biotin synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" cofactor metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"},{"category":"Process","description":" biotin metabolic process"},{"category":"Process","description":" biotin biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Radical_SAM","identifier":"PF04055"},{"name":"BATS","identifier":"PF06968"}],"pathways":[{"name":"Biotin metabolism","kegg_map_id":"00780"},{"name":"Biotin Biosynthesis","kegg_map_id":null}],"gene_sequence":"ATGATGTCTACTATCTACCGTCATTTATCTACCGCTAGACCGGCTTTAACTAAATACGCAACCAATGCCGCAGTTAAATCGACAACTGCATCCTCAGAAGCTAGTACTCTGGGTGCTCTACAATATGCATTGTCTTTAGATGAACCAAGTCATTCGTGGACAAAATCGCAATTAAAAGAAATTTATCATACCCCACTGCTCGAACTTACTCATGCAGCACAATTGCAGCACAGAAAGTGGCACGATCCAACCAAAGTGCAATTGTGCACATTGATGAACATCAAATCTGGTGGTTGTTCTGAGGACTGTAAGTATTGTGCGCAGTCTTCGAGAAACGATACCGGTCTAAAGGCTGAGAAAATGGTTAAAGTGGATGAAGTGATTAAAGAGGCAGAAGAGGCCAAAAGAAACGGATCTACTAGATTCTGCCTAGGTGCTGCATGGAGAGACATGAAAGGTCGTAAATCAGCCATGAAAAGAATTCAGGAAATGGTGACCAAAGTGAATGATATGGGGCTAGAAACGTGTGTTACTTTAGGTATGGTTGATCAAGATCAAGCAAAGCAATTGAAAGATGCAGGTTTGACTGCATACAACCATAACATCGACACTTCCAGAGAACACTATAGTAAGGTCATCACCACGAGAACCTACGACGACAGGTTACAGACCATCAAGAATGTCCAAGAATCTGGAATAAAAGCCTGTACCGGTGGTATTTTGGGTCTCGGTGAAAGCGAAGACGACCATATAGGATTCATCTACACATTATCCAATATGTCTCCTCATCCTGAGTCCCTACCAATTAATAGACTAGTTGCTATCAAAGGGACTCCAATGGCTGAGGAACTTGCCGATCCAAAGAGTAAAAAGTTGCAATTCGACGAAATTTTGAGAACCATTGCCACAGCGAGAATAGTTATGCCAAAGGCCATTATAAGACTTGCCGCTGGTCGTTATACAATGAAAGAAACAGAGCAATTTGTCTGTTTCATGGCAGGTTGTAACAGTATCTTCACCGGTAAGAAAATGCTGACGACAATGTGTAACGGTTGGGACGAAGACAAGGCAATGTTGGCTAAATGGGGATTGCAACCTATGGAGGCATTTAAGTACGACAGATCTTGA","protein_sequence":"MMSTIYRHLSTARPALTKYATNAAVKSTTASSEASTLGALQYALSLDEPSHSWTKSQLKEIYHTPLLELTHAAQLQHRKWHDPTKVQLCTLMNIKSGGCSEDCKYCAQSSRNDTGLKAEKMVKVDEVIKEAEEAKRNGSTRFCLGAAWRDMKGRKSAMKRIQEMVTKVNDMGLETCVTLGMVDQDQAKQLKDAGLTAYNHNIDTSREHYSKVITTRTYDDRLQTIKNVQESGIKACTGGILGLGESEDDHIGFIYTLSNMSPHPESLPINRLVAIKGTPMAEELADPKSKKLQFDEILRTIATARIVMPKAIIRLAAGRYTMKETEQFVCFMAGCNSIFTGKKMLTTMCNGWDEDKAMLAKWGLQPMEAFKYDRS"},{"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":" 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":"Function","description":" transferase activity"},{"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"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Radical_SAM","identifier":"PF04055"}],"pathways":[{"name":"Lipoic acid metabolism","kegg_map_id":"00785"}],"gene_sequence":"ATGTATAGACGATCTGTTGGAGTACTATTTGTTGGGAGAAATACAAGATGGATTTCGTCCACTATTAGGTGTGGAACGAGCGCAACTCGGCCAATAAGATCCAATGCATTGAATACTGATTCAGATAACGCTAGCGTTAGGGTACCAGTTGGAAATTCAACTGAGGTTGAAAATGCAACCAGTCAGTTAACAGGGACTTCGGGAAAAAGACGCAAGGGGAACAGAAAAAGAATTACAGAGTTCAAAGATGCTCTTAATTTGGGTCCATCTTTTGCAGATTTTGTTTCAGGTAAAGCTTCGAAAATGATCTTGGACCCTCTGGAGAAGGCAAGGCAAAATACAGAGGAAGCTAAAAAACTACCTCGTTGGCTTAAGGTTCCTATTCCTAAGGGTACCAATTACCATAAATTGAAAGGCGACGTAAAAGAATTAGGCCTGAGTACTGTTTGTGAGGAGGCAAGATGTCCCAATATTGGTGAATGTTGGGGAGGCAAAGATAAATCTAAGGCAACGGCAACAATTATGCTGCTTGGTGATACTTGCACTCGTGGATGTAGGTTTTGTTCTGTGAAGACCAATAGAACGCCTAGTAAGCCGGACCCAATGGAGCCCGAAAATACTGCCGAAGCTATCAAAAGATGGGGGTTGGGTTATGTTGTTTTAACTACCGTTGATAGGGACGATTTAGTCGATGGTGGTGCTAATCACCTGGCCGAGACGGTTCGCAAAATCAAACAGAAGGCACCAAATACTCTTGTAGAGACTCTTTCTGGTGATTTCAGAGGTGATTTGAAGATGGTGGACATTATGGCACAATGTGGGCTTGATGTTTACGCACATAATTTGGAAACAGTTGAATCACTAACACCACATGTCAGAGACAGAAGAGCTACTTATAGACAGTCTTTGAGTGTTTTAGAAAGGGCAAAAGCTACGGTTCCGTCACTGATTACTAAAACATCAATAATGCTGGGTCTAGGAGAAACTGATGAGCAAATTACTCAAACTTTGAAGGATTTGCGCAATATTCAATGTGATGTTGTTACATTTGGTCAATATATGAGGCCAACCAAGAGACATATGAAAGTCGTAGAATATGTGAAACCCGAAAAGTTTGACTACTGGAAAGAGAGAGCTTTAGAGATGGGATTCTTGTATTGTGCATCTGGACCCCTAGTAAGATCGTCATATAAGGCTGGTGAAGCATTTATTGAGAACGTTTTGAAGAAAAGAAACATGAAATAA","protein_sequence":"MYRRSVGVLFVGRNTRWISSTIRCGTSATRPIRSNALNTDSDNASVRVPVGNSTEVENATSQLTGTSGKRRKGNRKRITEFKDALNLGPSFADFVSGKASKMILDPLEKARQNTEEAKKLPRWLKVPIPKGTNYHKLKGDVKELGLSTVCEEARCPNIGECWGGKDKSKATATIMLLGDTCTRGCRFCSVKTNRTPSKPDPMEPENTAEAIKRWGLGYVVLTTVDRDDLVDGGANHLAETVRKIKQKAPNTLVETLSGDFRGDLKMVDIMAQCGLDVYAHNLETVESLTPHVRDRRATYRQSLSVLERAKATVPSLITKTSIMLGLGETDEQITQTLKDLRNIQCDVVTFGQYMRPTKRHMKVVEYVKPEKFDYWKERALEMGFLYCASGPLVRSSYKAGEAFIENVLKKRNMK"}]}