{"ymdb_id":"YMDB00363","created_at":"2011-05-29T18:09:52.000Z","updated_at":"2016-09-08T18:35:24.000Z","name":"Pyridoxal 5'-phosphate","cas":"54-47-7","state":"Solid","melting_point":"255 oC","description":"Pyridoxal 5'-phosphate (PLP, vitamin B6) 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":"28 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"18405","hmdb_id":"HMDB01491","kegg_id":"C00018","pubchem_id":"1051","cs_id":"1022","foodb_id":null,"wikipedia_link":"Pyridoxal_phosphate","biocyc_id":"PYRIDOXAL_PHOSPHATE","iupac":"[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid","traditional_iupac":"pyridoxal phosphate","logp":"-2.0856087036128135","pka":"6.691277029499376","alogps_solubility":"5.70e+00 g/l","alogps_logp":"-0.55","alogps_logs":"-1.64","acceptor_count":"6","donor_count":"3","rotatable_bond_count":"4","polar_surface_area":"116.95","refractivity":"54.746300000000005","polarizability":"20.898887181263255","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"4.109012435085948","pka_strongest_acidic":"1.680298610655746","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["Apolon B6","Biosechs","Codecarboxylase","Coenzyme B6","Hairoxal","Hexermin-P","Hi-Pyridoxin","Hiadelon","Himitan","PAL-P","Phosphopyridoxal","Phosphopyridoxal coenzyme","Pidopidon","Piodel","PLP","Pydoxal","Pyridoxal 5-phosphate","Pyridoxal 5'-phosphate","Pyridoxal 5'-phosphic acid","Pyridoxal P","Pyridoxal phosphate","Pyridoxal-P","Pyridoxyl phosphate","Pyromijin","Sechvitan","Vitahexin-P","Vitazechs"],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"},{"name":"Porphyrin Metabolism","kegg_map_id":null},{"name":"Sphingolipid metabolism","kegg_map_id":"00600"},{"name":"Starch and sucrose metabolism","kegg_map_id":"00500"},{"name":"Sulfur metabolism","kegg_map_id":"00920"},{"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":" 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":"Function","description":" oxidoreductase activity"},{"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"},{"category":"Process","description":" oxidation reduction"}],"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"},{"created_at":"2011-05-26T20:16:27.000Z","updated_at":"2011-05-27T15:01:08.000Z","name":"Putative pyridoxal kinase BUD16","uniprot_id":"P39988","uniprot_name":"BUD16_YEAST","enzyme":true,"transporter":false,"gene_name":"BUD16","num_residues":312,"molecular_weight":"35558.89844","theoretical_pi":"6.51","general_function":"Involved in pyridoxal kinase activity","specific_function":"Required for synthesis of pyridoxal-5-phosphate from vitamin B6. Important for bud site selection","reactions":[{"id":2592,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"U18530","genbank_protein_id":"602396","gene_card_id":"BUD16","chromosome_location":"chromosome 5","locus":"YEL029C","synonyms":["Bud site selection protein 16"],"enzyme_classes":["2.7.1.35"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" pyridoxal kinase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" kinase activity"},{"category":"Process","description":" vitamin B6 metabolic process"},{"category":"Process","description":" pyridoxine metabolic process"},{"category":"Process","description":" pyridoxine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"}],"pfams":[{"name":"Phos_pyr_kin","identifier":"PF08543"}],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"}],"gene_sequence":"ATGCCTCGTCTCTTGGCCACGCAGTCTCATGTTGTACATGGATATGTGGGAAATAAGGCTGCAACGTTTCCCTTACAGTGTCTAGGCTGGGATGTGGATTGTTGTAACAGTGTTCAGTTTTCCAACCATACCGGATATGGTTTAGATAAAGTGTTTGGGACTATAACGAGGGAAACAGATTTGAAGGAACTCTTATCAGGTCTTTTTGATAATTTTTCCCAAGACTACCAAGCCTTACTTTCAGGCTACTTGCCCAATAAGAATTCCGTTCGATGTATGGGAACATACTACGCTAAATTTAAAGAGGCGAATCCAGAAATGATATGGCTTATGGATCCTGTTATGGGTGACGAAGGACAATTATATGTTAGTGAGGATGTCATACCAGAATATAGAAAGCTGGCTTTGTCTCCAAAACAGCTAGTCGATATAATAACTCCGAATCAATTTGAGCTGGAGATACTTTATGGGGGGGAAATCAAGACTAAAGAACATTTGAAGAAGGCCTTAAAGAAATTACACCAAACTATCCCAGTGATCATTGTCACATCCTGTGACTGTAAGATGTTTGATGACAAAGATTTTATTTATTGCGTAGCTTCAATGGAGGGTAAAACCCCCATTGTTTACAGAGTGCCGTTTATTGATTCGTATTTCACTGGGGTTGGTGATTTGTTTTCTGCTTTGTTATTGGATCGAGTGTATAAGATCTTATCGAACCCTACAACAACATTAAAATTTGAAGACCAAGTCAATAATGTTCTTAATGTTATTCAGAAGGTTTTGAAAATTACTAGGAGCTATGCTTCAGGAAAAATGAAAGCAAAAATGGGTTCCGCCTTGGAAATGAAAGAAATGGAATTGCGTCTTATTGAATCAAGAGATATATATGAAACAATCAACATTCATCAAACAGATTATATTTACGCAAGGTTGTGA","protein_sequence":"MPRLLATQSHVVHGYVGNKAATFPLQCLGWDVDCCNSVQFSNHTGYGLDKVFGTITRETDLKELLSGLFDNFSQDYQALLSGYLPNKNSVRCMGTYYAKFKEANPEMIWLMDPVMGDEGQLYVSEDVIPEYRKLALSPKQLVDIITPNQFELEILYGGEIKTKEHLKKALKKLHQTIPVIIVTSCDCKMFDDKDFIYCVASMEGKTPIVYRVPFIDSYFTGVGDLFSALLLDRVYKILSNPTTTLKFEDQVNNVLNVIQKVLKITRSYASGKMKAKMGSALEMKEMELRLIESRDIYETINIHQTDYIYARL"},{"created_at":"2011-05-26T20:26:05.000Z","updated_at":"2011-05-27T15:01:09.000Z","name":"Putative pyridoxal kinase BUD17","uniprot_id":"P53727","uniprot_name":"BUD17_YEAST","enzyme":true,"transporter":false,"gene_name":"BUD17","num_residues":317,"molecular_weight":"35366.5","theoretical_pi":"6.78","general_function":"Involved in pyridoxal kinase activity","specific_function":"Required for synthesis of pyridoxal-5-phosphate from vitamin B6. Important for bud site selection","reactions":[{"id":2592,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"AY692946","genbank_protein_id":"51013343","gene_card_id":"BUD17","chromosome_location":"chromosome 14","locus":"YNR027W","synonyms":["Bud site selection protein 17"],"enzyme_classes":["2.7.1.35"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" pyridoxal kinase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" kinase activity"},{"category":"Process","description":" vitamin B6 metabolic process"},{"category":"Process","description":" pyridoxine metabolic process"},{"category":"Process","description":" pyridoxine biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" small molecule metabolic process"},{"category":"Process","description":" vitamin metabolic process"},{"category":"Process","description":" water-soluble vitamin metabolic process"}],"pfams":[{"name":"Phos_pyr_kin","identifier":"PF08543"}],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"}],"gene_sequence":"ATGACCAGTACATTACATACGACAAAAAAAGTGCTCTCCATTCAATCACACGTCATACATGGCTACGTGGGAAACAAGGCCGCTACGTTCCCACTTCAATACAGAGGTTGGGATGTGGACGTATTGAACACAGTTCAGTTTTCTAACCACTCGGGGTACGCCCACTTCACAGGCTTCAAATGCAGCACTGAGGAGTTGGTAGACATTGTAGAGAAGGGCTTGATTGGGTCTCTTAGAATCAAGTATGATGCCGTACTTAGTGGCTATTTACCCAATGGTCAAGCCCTGCAAAAGGTAGCAGGAATAGTGGGTCAATTATGTGAGGGGAGTGAAAACGTCAAGTGGATATTAGATCCTGTACTGGGCGATAATGGAAGGCTGTACGTGGATCGAGAATGTGTTGCGGTATACCAAGACATTTTACAAAACTTCAAAATTTTTTTGGCCACACCAAATCAGTTTGAAATGGAACTGTTGGTGGGGATGTCAATTCGTACCTTAGACGACGCTAAGCAGGCATTTAAACTATTTCATAAAAAGTACCCTCGAGTAAGCCGAATAGTTGTCACTAGTCTGGAATTATCTGAATTCCTGAGCAACGACACTTACGTAGTAGCAGGGTTTGATTGCTCGGCCAGTGAAGAGATATTCTTCTATGAAATCCCCAAGATCAACGCAAAATTTAGTGGAAGTGGTGATTTAATCAGCGCCATGCTCACTGACTCGTTACTAGGCGACCGCCGCTGCACACAGCTGTCATTAAGCGCATCCTTGGGCCAAGTGCTGTGGCTCGTCACCAGTATCCTACAAAAAACGTATGATTTAAACATAGCTGAGCGGGGCCCACAAGATTCCACGATAGATATCAAGGATTTAAAGCTGATTCAGTGTAGAGACATCCTAAAGCAAGATCTCATACCCTCCATTGGCAAGCCAAAAACCATTAAAATATGA","protein_sequence":"MTSTLHTTKKVLSIQSHVIHGYVGNKAATFPLQYRGWDVDVLNTVQFSNHSGYAHFTGFKCSTEELVDIVEKGLIGSLRIKYDAVLSGYLPNVQALQKVAGIVGQLCEGSENVKWILDPVLGDNGRLYVDRECVAVYQDILQNFKIFLATPNQFEMELLVGMSIRTLDDAKQAFKLFHKKYPRVSRIVVTSLELSEFLSNDTYVVAGFDCSASEEIFFYEIPKINAKFSGSGDLISAMLTDSLLGDRRCTQLSLSASLGQVLWLVTSILQKTYDLNIAERGPQDSTIDIKDLKLIQCRDILKQDLIPSIGKPKTIKI"}]}