{"ymdb_id":"YMDB00037","created_at":"2011-05-29T15:50:35.000Z","updated_at":"2016-10-18T17:11:15.000Z","name":"Pyridoxine","cas":"65-23-6","state":"Solid","melting_point":"159-162oC","description":"Pyridoxine is the 4-methanol form of pyridoxal 5'-phosphate (PLP, vitamin B6). Pyridoxal 5'-phosphate is a coenzyme for many enzymes that participate in amino acid and glycogen metabolism. Pyridoxal 5'-phosphate can be synthesized de novo and by salvage pathways from pyridoxal, pyroxidine and pyridoxamine that might be present in the environment. [Biocyc PLPSAL-PWY]","experimental_water_solubility":"79 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":"-0.77 [SANGSTER (1993)]","location":"extracellular;cytoplasm","synthesis_reference":"Itov, Z. I.; Stepanova, S. V.; El'yanov, B. S.; Gunar, V. I.  Synthesis of pyridoxine under high pressure.    Khimiko-Farmatsevticheskii Zhurnal  (1987),  21(7),  858-62.","chebi_id":"16709","hmdb_id":"HMDB00239","kegg_id":"C00314","pubchem_id":"1054","cs_id":"1025","foodb_id":null,"wikipedia_link":"Pyridoxine","biocyc_id":"CPD-455","iupac":"4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol","traditional_iupac":"pyridoxine","logp":"-0.9513212983333332","pka":"14.533140285427315","alogps_solubility":"1.61e+01 g/l","alogps_logp":"-0.57","alogps_logs":"-1.02","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"73.58000000000001","refractivity":"44.1053","polarizability":"17.112304740817216","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"5.584997111043129","pka_strongest_acidic":"9.397430003835803","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine","2-Methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine","2-Methyl-3-hydroxy-4,5-dihydroxymethylpyridine","2-Methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine","3-hydroxy-2-Picoline-4,5-dimethanol","3-Hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine","3-Hydroxy-4,5-dimethylol-a-picoline","3-Hydroxy-4,5-dimethylol-alpha-picoline","3-Hydroxy-4,5-dimethylol-α-picoline","5-Hydroxy-6-methyl-3,4-pyridinedimethanol","Adermine","Gravidox","Hydoxin","Piridossina","Piridoxina","Pyridoxin","Pyridoxine","Pyridoxine hydrochloride","Pyridoxinum","Pyridoxol","Pyridoxol hydrochloride","Pyridoxolum","Rodex","Vitamin b6"],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"},{"name":"Vitamin B6","kegg_map_id":null}],"growth_conditions":[{"growth_media":"hops, malted barley","concentration":"3.0","concentration_units":"\u0026#181;M","error":"0.0"},{"growth_media":"grape juice","concentration":"3.0","concentration_units":"\u0026#181;M","error":"0.0"}],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"pubmed_id":21062828,"citation":"Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). \"BRENDA, the enzyme information system in 2011.\" Nucleic Acids Res 39:D670-D676."},{"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":null,"citation":"Alcoholic beverage, beer, regular, all - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. \u003ca href = http://www.ars.usda.gov/ba/bhnrc/ndl\u003eNutrient Data Laboratory Home Page\u003c/a\u003e"},{"pubmed_id":null,"citation":"Alcoholic beverage, wine, table, red - U.S. Department of Agriculture, Agricultural Research Service. 2010. USDA National Nutrient Database for Standard Reference, Release 23. \u003ca href = http://www.ars.usda.gov/ba/bhnrc/ndl\u003eNutrient Data Laboratory Home Page\u003c/a\u003e"},{"pubmed_id":12649274,"citation":"Stolz, J., Vielreicher, M. (2003). \"Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae.\" J Biol Chem 278:18990-18996."}],"proteins":[{"created_at":"2011-05-24T20:59:48.000Z","updated_at":"2011-05-24T20:59:48.000Z","name":"Putative pyridoxal reductase","uniprot_id":"Q06494","uniprot_name":"PLR1_YEAST","enzyme":true,"transporter":false,"gene_name":null,"num_residues":345,"molecular_weight":"38600.39844","theoretical_pi":"5.85","general_function":"Involved in oxidoreductase activity","specific_function":"Catalyzes the reduction of pyridoxal (PL) with NADPH and oxidation of pyridoxine (PN) with NADP(+)","reactions":[{"id":2355,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"Pyridoxine + NADP(+) = pyridoxal + NADPH.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"U40828","genbank_protein_id":"1066468","gene_card_id":null,"chromosome_location":null,"locus":"YPR127W","synonyms":["PL reductase","PL-red"],"enzyme_classes":["1.1.1.65"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" oxidation reduction"}],"pfams":[{"name":"Aldo_ket_red","identifier":"PF00248"}],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"}],"gene_sequence":"ATGTCTGTCGCCGATTTGAAAAACAACATCCACAAGTTAGATACTGGCTATGGTTTAATGAGTTTGACTTGGAGAGCCGAGCCTATCCCTCAGTCGCAGGCTTTCGAGGCCATGCACAGAGTGGTTGAGTTATCCAGAGAACGTGGGCACAAGGCCTTTTTCAACGTTGGTGAATTCTATGGTCCCGATTTTATTAATTTGTCGTATGTTCACGACTTCTTTGCGAAATACCCAGATTTGAGAAAGGATGTGGTTATCAGTTGTAAAGGTGGTGCAGACAATGCTACCTTAACCCCCAGAGGCAGTCACGATGATGTTGTACAAAGCGTAAAGAATTCAGTTAGTGCTATTGGTGGCTACATCGACATCTTCGAAGTCGCAAGAATCGACACTTCCCTATGCACGAAAGGAGAGGTCTACCCCTACGAATCGTTCGAAGCGCTTGCTGAGATGATCTCCGAAGGCGTTATTGGCGGTATTTCATTAAGTGAAGTTAATGAAGAGCAAATTAGAGCTATTCACAAGGATTGGGGAAAGTTTTTGACCTGCGTTGAAGTGGAACTTTCTTTGTTCAGTAATGACATTTTACACAACGGAATTGCTAAAACATGTGCTGAATTGGGGTTGTCCATCATCTGCTACTCCCCACTGGGCAGAGGATTGTTGACAGGTCAATTGAAGTCAAACGCTGATATCCCTGAGGGTGACTTTAGAAAGTCGTTAAAGAGATTTAGCGACGAGTCTTTGAAAAAAAACCTGACCTTGGTCAGGTTTCTACAGGAAGAAATAGTCGACAAGCGCCCACAAAACAACTCCATTACTCTTGCACAACTGGCTTTGGGATGGGTTAAGCACTGGAACAAAGTTCCGGAATACAGTGGCGCCAAATTTATCCCAATTCCAAGTGGCTCTTCTATTTCCAAGGTTAATGAAAACTTTGATGAACAGAAAACCAAACTTACCGATCAAGAGTTCAATGCCATTAACAAATATTTGACTACTTTCCATACTGTTGGTGACAGATACGAAATGGCGTAA","protein_sequence":"MSVADLKNNIHKLDTGYGLMSLTWRAEPIPQSQAFEAMHRVVELSRERGHKAFFNVGEFYGPDFINLSYVHDFFAKYPDLRKDVVISCKGGADNATLTPRGSHDDVVQSVKNSVSAIGGYIDIFEVARIDTSLCTKGEVYPYESFEALAEMISEGVIGGISLSEVNEEQIRAIHKDWGKFLTCVEVELSLFSNDILHNGIAKTCAELGLSIICYSPLGRGLLTGQLKSNADIPEGDFRKSLKRFSDESLKKNLTLVRFLQEEIVDKRPQNNSITLAQLALGWVKHWNKVPEYSGAKFIPIPSGSSISKVNENFDEQKTKLTDQEFNAINKYLTTFHTVGDRYEMA"},{"created_at":"2011-05-24T21:00:19.000Z","updated_at":"2011-05-27T15:00:57.000Z","name":"Vitamin B6 transporter TPN1","uniprot_id":"P53099","uniprot_name":"TPN1_YEAST","enzyme":true,"transporter":false,"gene_name":"TPN1","num_residues":579,"molecular_weight":"64545.80078","theoretical_pi":"8.83","general_function":"Involved in nucleobase transmembrane transporter activity","specific_function":"Thiamine-regulated, high affinity import carrier of pyridoxine, pyridoxal and pyridoxamine","reactions":[],"signal_regions":"None","transmembrane_regions":"99-119;123-143;158-178;199-219;222-242;275-295;303-323;363-383;395-415;422-442;520-540;546-566","pdb_id":null,"cellular_location":"Membrane; Multi-pass membrane protein","genbank_gene_id":"X91489","genbank_protein_id":"1143561","gene_card_id":"TPN1","chromosome_location":"chromosome 7","locus":"YGL186C","synonyms":["Transport of pyridoxine protein 1"],"enzyme_classes":[],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" membrane"},{"category":"Function","description":" substrate-specific transmembrane transporter activity"},{"category":"Function","description":" nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity"},{"category":"Function","description":" nucleobase transmembrane transporter activity"},{"category":"Function","description":" transporter activity"},{"category":"Function","description":" transmembrane transporter activity"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid transport"},{"category":"Process","description":" transmembrane transport"},{"category":"Process","description":" establishment of localization"},{"category":"Process","description":" transport"}],"pfams":[{"name":"Transp_cyt_pur","identifier":"PF02133"}],"pathways":[],"gene_sequence":"ATGAATAGGGACAACATGGACACAACAAAGCGCAAAGAAGATCATACAAAGCATACTACTGATGTAATAGAATTTTACGAAGAAGGAACCGCAGCTTCTTCTTTAAACATAGCCACAGAAAAGGCCAACTCAAGTCCGTCCATTTTGAGAAGAATTATCAACAGGGCGGCATGGCTTTCTAAGAAAGTGGACGCAATGGGAGTAGAGTCTACCGGTATTCAGAGGATATCTCCCTATGAACGAGGAACATCAAAGAAACAATTTTTGCATGTCGCGGGGCTATGGTTGAGTGCCACAGGTGGTTTGTCTTCCATGTCGTCGTTTTTATTAGGCCCTCTGCTTTTCGGTTTAAGCTTTAGAGAATCCGTAGCCTCCAGTTTAATATCGGTAACAATTGGTTGCTTAATTGCTGCCTATTGCTCGATCATGGGACCGCAGTCCGGTTGCAGACAGATGGTAACAGCTAGATACCTGTTCGGATGGTGGTTTGTTAAATTAGTTGCATTAGCTTCCATTATCGGTGTCATGGGTTGGTCTGTGGTTAATTCCGTGGTTGGGGGTGAAATGTTAGCTGCTATTTCTAATGATAAAGTACCCCTATGGGTAGGGATTGTCATAGTGACCGTATGCTCCTTTTTAGTTGCCATTTTCGGTATCAAACAAGTCATTAAAGTGGAAACTTACTTATCCGTACCCGTCCTGACAGCATTTTTACTACTGTACATTTCATCAAGTGATAAATACAGCTTCGTCAATGCATACGTTTCAAAGGGAAATTTGGACTCTTCCACCCGAAAGGGCAACTGGATGAGTTTTTTTTCATTATGCTATAGTATTACGGCTACTTGGGGGTCTATTACAGCAGACTATTATATATTGTTCCCAGAAGATACACCATATATTCAAATTTTTTGCCTAACGTTTTTTGGAACATTTTTGCCTACCTGTTTCGTCGGAATCTTAGGTCTCTTACTAGCTTCTGTTGCCATGTCGTATAAGCCTTGGTCAGTCGAGTACGATTCCCATGGAATGGGTGGTCTACTTTGGGCAGGTTTTCAGCGTTGGAACGGCTTCGGAAAGTTCTGCGTGGTAGTACTGGTATTCAGTTTGGTATCCAACAACATCATCAATACGTATTCGGCAGCATTCTCCATCCAACTTTCTAGTGTGTTTTGTGCAAAAATCCCTCGCTGGTTCTGGTCTATTGTTTGTACTATAATTTGTTTGGTATGCGCATTAATAGGTCGTAATCATTTTAGTACTATTTTGGGAAATTTCCTACCAATGATAGGCTACTGGATTAGCATGTACTTTATCTTATTATTCGAAGAGAATTTAGTATTCAGAAGGTTTTTCTTACATTTGTACACCAAAGAGTTTCCTACAGTTACAGGAGAAATAAATGGACCGGAACTTGTTGGATCTTCAAAAGAAGTGGAGAAAGATGCAGTTACTAATATCCATTTGTTAAAAAGAAAACATAAGGTGACTAAACATCGTTACAATTGGGACAAATGGGAAGATTATGAGGTTTTAACGCACGGTTATGCAGCAACATTTGCGTTTATTGTAGGAGTTGCTGGTGTGGTAGTTGGTATGGCGCAAGCCTATTGGATTGGCCCAATTGCTGCCAAATTTGGTGAATATGGTGGTGATGTCGCAATGTGGTTAAGTATGGCGTTCTCAGGTGTTGTATACCCTCCTTGTAGATACTTAGAGCTACGTAAATTTGGTCGTTAA","protein_sequence":"MNRDNMDTTKRKEDHTKHTTDVIEFYEEGTAASSLNIATEKANSSPSILRRIINRAAWLSKKVDAMGVESTGIQRISPYERGTSKKQFLHVAGLWLSATGGLSSMSSFLLGPLLFGLSFRESVASSLISVTIGCLIAAYCSIMGPQSGCRQMVTARYLFGWWFVKLVALASIIGVMGWSVVNSVVGGEMLAAISNDKVPLWVGIVIVTVCSFLVAIFGIKQVIKVETYLSVPVLTAFLLLYISSSDKYSFVNAYVSKGNLDSSTRKGNWMSFFSLCYSITATWGSITADYYILFPEDTPYIQIFCLTFFGTFLPTCFVGILGLLLASVAMSYKPWSVEYDSHGMGGLLWAGFQRWNGFGKFCVVVLVFSLVSNNIINTYSAAFSIQLSSVFCAKIPRWFWSIVCTIICLVCALIGRNHFSTILGNFLPMIGYWISMYFILLFEENLVFRRFFLHLYTKEFPTVTGEINGPELVGSSKEVEKDAVTNIHLLKRKHKVTKHRYNWDKWEDYEVLTHGYAATFAFIVGVAGVVVGMAQAYWIGPIAAKFGEYGGDVAMWLSMAFSGVVYPPCRYLELRKFGR"},{"created_at":"2011-05-24T21:00:56.000Z","updated_at":"2011-05-27T15:00:57.000Z","name":"Pyridoxamine 5'-phosphate oxidase","uniprot_id":"P38075","uniprot_name":"PDX3_YEAST","enzyme":true,"transporter":false,"gene_name":"PDX3","num_residues":228,"molecular_weight":"26908.0","theoretical_pi":"7.67","general_function":"Involved in pyridoxamine-phosphate oxidase activity","specific_function":"Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP)","reactions":[{"id":1923,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1924,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1926,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1928,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2356,"direction":"\u003e","locations":null,"altext":"Pyridoxamine 5'-phosphate + H(2)O + O(2) = pyridoxal 5'-phosphate + NH(3) + H(2)O(2).","export":false,"pw_reaction_id":null,"source":null},{"id":2357,"direction":"\u003e","locations":null,"altext":"Pyridoxine 5'-phosphate + O(2) = pyridoxal 5'-phosphate + H(2)O(2).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1CI0","cellular_location":null,"genbank_gene_id":"AY557712","genbank_protein_id":"45269315","gene_card_id":"PDX3","chromosome_location":"chromosome 2","locus":"YBR035C","synonyms":["PNP/PMP oxidase","PNPOx"],"enzyme_classes":["1.4.3.5"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor"},{"category":"Function","description":" pyridoxamine-phosphate oxidase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleotide binding"},{"category":"Function","description":" FMN binding"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-NH2 group of donors"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"},{"category":"Process","description":" vitamin B6 metabolic process"},{"category":"Process","description":" pyridoxine metabolic process"},{"category":"Process","description":" pyridoxine biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"PNPOx_C","identifier":"PF10590"},{"name":"Pyridox_oxidase","identifier":"PF01243"}],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"}],"gene_sequence":"ATGACTAAACAAGCTGAGGAGACCCAAAAGCCAATCATATTTGCTCCTGAGACGTATCAATATGATAAATTTACTTTGAATGAAAAACAACTTACTGACGACCCAATCGATCTTTTCACCAAATGGTTCAACGAAGCCAAGGAAGACCCAAGGGAAACGTTGCCAGAAGCAATTACTTTTTCATCCGCGGAACTACCTAGTGGGAGGGTGTCGTCCAGGATTCTTCTTTTTAAGGAGCTCGACCATAGAGGTTTTACTATTTATTCTAACTGGGGAACCTCTAGAAAGGCTCATGATATTGCTACCAACCCGAATGCGGCAATCGTATTCTTTTGGAAGGATCTGCAAAGGCAGGTGAGAGTTGAAGGTATCACAGAGCATGTTAACAGAGAAACTTCTGAAAGATACTTTAAGACGAGACCTCGTGGATCCAAGATCGGTGCATGGGCTTCCCGCCAATCGGATGTTATCAAGAACAGAGAAGAACTAGACGAGTTGACCCAAAAAAACACCGAACGTTTCAAGGATGCTGAAGACATCCCATGTCCAGATTATTGGGGTGGCTTGAGAATCGTTCCACTGGAAATTGAGTTCTGGCAAGGTAGACCCTCGAGATTGCATGATAGATTCGTTTACAGAAGAAAAACAGAAAACGATCCATGGAAAGTCGTTAGACTAGCCCCATGA","protein_sequence":"MTKQAEETQKPIIFAPETYQYDKFTLNEKQLTDDPIDLFTKWFNEAKEDPRETLPEAITFSSAELPSGRVSSRILLFKELDHRGFTIYSNWGTSRKAHDIATNPNAAIVFFWKDLQRQVRVEGITEHVNRETSERYFKTRPRGSKIGAWASRQSDVIKNREELDELTQKNTERFKDAEDIPCPDYWGGLRIVPLEIEFWQGRPSRLHDRFVYRRKTENDPWKVVRLAP"}]}