{"ymdb_id":"YMDB00407","created_at":"2011-05-29T18:13:46.000Z","updated_at":"2016-09-08T18:35:27.000Z","name":"Pyridoxine 5'-phosphate","cas":"447-05-2","state":"Solid","melting_point":"","description":"Pyridoxine 5'-phosphate is an intermediate in pyridoxal 5'-phosphate salvage pathway. 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":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Argoudelis, Chris J. Preparation of crystalline pyridoxine 5'-phosphate and some of its properties. Journal of Agricultural and Food Chemistry (1986), 34(6), 995-8.","chebi_id":"28803","hmdb_id":"HMDB01319","kegg_id":"C00627","pubchem_id":"1055","cs_id":"1026","foodb_id":null,"wikipedia_link":null,"biocyc_id":"PYRIDOXINE-5P","iupac":"{[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methoxy}phosphonic acid","traditional_iupac":"pyridoxine-5'-phosphate","logp":"-3.640999575634358","pka":"6.798869153656689","alogps_solubility":"9.41e+00 g/l","alogps_logp":"-0.80","alogps_logs":"-1.42","acceptor_count":"6","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"120.11000000000001","refractivity":"54.97820000000001","polarizability":"21.726701172777485","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"5.554512423881395","pka_strongest_acidic":"1.7391293357611506","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphate","5-hydroxy-6-methyl-3,4-Pyridinedimethanol alpha( 3)-(dihydrogen phosphate)","Pyridoxine 5-phosphate","Pyridoxine 5'-phosphate","Pyridoxine 5'-phosphic acid","Pyridoxine-5'-phosphate","pyridoxine-5P","pyridoxine-P","pyridoxine-phosphate","Pyridoxol 5-phosphate","Pyridoxyl-5-phosphate"],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"},{"name":"Vitamin B6","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."},{"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."}],"proteins":[{"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":" 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":"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":"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"}]}