{"ymdb_id":"YMDB00889","created_at":"2011-05-29T19:01:37.000Z","updated_at":"2016-09-08T18:36:01.000Z","name":"Pyridoxamine","cas":"85-87-0","state":"Solid","melting_point":null,"description":"Pyridoxamine is the 4-aminomethyl 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":"815 mg/mL [HMP experimental]","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":null,"chebi_id":"16410","hmdb_id":"HMDB01431","kegg_id":"C00534","pubchem_id":"1052","cs_id":"1023","foodb_id":null,"wikipedia_link":"Piridoxamine","biocyc_id":"PYRIDOXAMINE","iupac":"4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol","traditional_iupac":"pyridoxamine","logp":"-1.6069905405485954","pka":"14.85255410474139","alogps_solubility":"2.90e+01 g/l","alogps_logp":"-1.23","alogps_logs":"-0.76","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"79.37","refractivity":"45.76279999999999","polarizability":"17.524325285309423","formal_charge":"0","physiological_charge":"1","pka_strongest_basic":"9.612992220108088","pka_strongest_acidic":"7.809408884689676","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2-methyl-4-aminomethyl-5-hydroxymethyl-3-Pyridinol","4-(Aminomethyl)-5-(hydroxymethyl)-2-methyl-3-pyridinol","4-(aminomethyl)-5-hydroxy-6-methyl-3-Pyridinemethanol","PM","Pyridoxylamine"],"pathways":[{"name":"Vitamin B6 metabolism","kegg_map_id":"00750"},{"name":"Vitamin B6","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":12713350,"citation":"Zeidler, J., Gupta, R. N., Sayer, B. G., Spenser, I. D. (2003). \"Biosynthesis of Vitamin B(6) in yeast. Incorporation pattern of trioses.\" J Org Chem 68:3486-3493."}],"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"}]}