{"ymdb_id":"YMDB00145","created_at":"2011-05-29T16:01:20.000Z","updated_at":"2016-09-08T18:35:05.000Z","name":"Hydroxymethylbilane","cas":"73023-76-4","state":"Solid","melting_point":null,"description":"Hydroxymethylbilane is the precursor to uroporphyrinogen-III in tetrapyrrole biosynthesis pathway which starts with the formation of 5-aminolevulinic acid from glycine and succinyl CoA by the enzyme ALA synthase. Uroporphyrinogen-III is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Tetrapyrroles usually function as a metal-binding cofactor in many important enzymes, proteins and pigments, such as heme, chlorophyll, cobalamine, siroheme, and cofator F430. [Biocyc PWY-5189] ","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":null,"chebi_id":"16645","hmdb_id":"HMDB01137","kegg_id":"C01024","pubchem_id":"788","cs_id":"767","foodb_id":null,"wikipedia_link":"Hydroxymethylbilane","biocyc_id":"HYDROXYMETHYLBILANE","iupac":"3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid","traditional_iupac":"3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid","logp":"0.9672566426666659","pka":"3.626386055193484","alogps_solubility":"3.23e-02 g/l","alogps_logp":"0.53","alogps_logs":"-4.42","acceptor_count":"17","donor_count":"13","rotatable_bond_count":"27","polar_surface_area":"381.78999999999996","refractivity":"209.9212000000002","polarizability":"85.68481619191945","formal_charge":"0","physiological_charge":"-8","pka_strongest_basic":null,"pka_strongest_acidic":"3.253943717832704","bioavailability":"0","number_of_rings":"4","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["3-[2-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoate","3-[2-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoic acid","3,8,13,18-tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoate","3,8,13,18-tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoic acid","3,8,13,18-tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoate","3,8,13,18-tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoic acid","hydroxymethylbilane","Preuroporphyrinogen"],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"},{"name":"Porphyrin Metabolism","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":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":8234090,"citation":"Chelstowska, A., Rytka, J. (1993). \"[Biosynthesis of heme in yeast Saccharomyces cerevisiae].\" Postepy Biochem 39:173-185."},{"pubmed_id":14559249,"citation":"Hoffman, M., Gora, M., Rytka, J. (2003). \"Identification of rate-limiting steps in yeast heme biosynthesis.\" Biochem Biophys Res Commun 310:1247-1253."}],"proteins":[{"created_at":"2011-05-26T18:11:47.000Z","updated_at":"2011-05-27T15:01:03.000Z","name":"Porphobilinogen deaminase","uniprot_id":"P28789","uniprot_name":"HEM3_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM3","num_residues":327,"molecular_weight":"36674.19922","theoretical_pi":"6.32","general_function":"Involved in hydroxymethylbilane synthase activity","specific_function":"Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps","reactions":[{"id":1647,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2515,"direction":"\u003e","locations":null,"altext":"4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X99000","genbank_protein_id":"1429351","gene_card_id":"HEM3","chromosome_location":"chromosome 4","locus":"YDL205C","synonyms":["PBG","Hydroxymethylbilane synthase","HMBS","Pre-uroporphyrinogen synthase"],"enzyme_classes":["2.5.1.61"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring alkyl or aryl (other than methyl) groups"},{"category":"Function","description":" hydroxymethylbilane synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" macromolecule metabolic process"},{"category":"Process","description":" macromolecule modification"},{"category":"Process","description":" protein modification process"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular biosynthetic process"},{"category":"Process","description":" heterocycle biosynthetic process"},{"category":"Process","description":" tetrapyrrole biosynthetic process"},{"category":"Process","description":" post-translational protein modification"},{"category":"Process","description":" protein-cofactor linkage"},{"category":"Process","description":" peptidyl-pyrromethane cofactor linkage"}],"pfams":[{"name":"Porphobil_deam","identifier":"PF01379"},{"name":"Porphobil_deamC","identifier":"PF03900"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGGGCCCTGAAACTCTACATATTGGTGGGAGAAAATCGAAATTGGCGGTAATACAATCCAACCATGTTTTAAAACTGATCGAAGAAAAGTATCCGGACTACGACTGCAAGGTTTTCACTTTGCAAACTCTTGGTGACCAGATTCAATTCAAACCTTTGTACTCATTTGGCGGTAAAGCTTTATGGACAAAGGAGTTGGAAGACCATCTTTACCATGACGATCCCTCAAAGAAGCTTGACTTGATCGTTCATTCTCTGAAGGACATGCCCACTTTACTACCAGAGGGTTTCGAGCTGGGGGGTATCACTAAGCGGGTCGATCCAACAGATTGTCTTGTCATGCCCTTTTACTCTGCTTATAAGTCTCTGGATGACCTTCCAGACGGGGGGATTGTGGGAACCTCATCCGTGAGAAGATCTGCTCAGCTAAAAAGAAAATACCCACATTTGAAATTTGAAAGTGTCAGAGGAAATATACAAACTAGATTACAAAAACTAGACGACCCAAAATCTCCGTACCAATGCATCATCTTGGCGTCTGCTGGGTTGATGCGTATGGGGTTGGAAAACAGAATTACGCAGCGATTCCATTCGGATACAATGTACCATGCAGTTGGACAAGGCGCCCTGGGTATAGAAATTAGAAAGGGTGACACCAAGATGATGAAGATTCTTGACGAAATTTGCGATCTAAATGCAACTATATGTTGCCTTTCGGAGCGTGCTTTGATGAGAACTTTAGAGGGGGGTTGTTCCGTTCCTATTGGTGTGGAATCTAAATACAATGAAGAGACTAAAAAATTACTATTAAAGGCCATTGTAGTTGACGTTGAAGGCACAGAAGCAGTAGAAGACGAAATTGAAATGCTAATAGAAAATGTTAAAGAAGATTCCATGGCGTGTGGTAAGATACTAGCTGAAAGAATGATTGCCGATGGCGCAAAGAAAATTCTGGATGAAATTAATTTAGACAGAATCAAATGA","protein_sequence":"MGPETLHIGGRKSKLAVIQSNHVLKLIEEKYPDYDCKVFTLQTLGDQIQFKPLYSFGGKALWTKELEDHLYHDDPSKKLDLIVHSLKDMPTLLPEGFELGGITKRVDPTDCLVMPFYSAYKSLDDLPDGGIVGTSSVRRSAQLKRKYPHLKFESVRGNIQTRLQKLDDPKSPYQCIILASAGLMRMGLENRITQRFHSDTMYHAVGQGALGIEIRKGDTKMMKILDEICDLNATICCLSERALMRTLEGGCSVPIGVESKYNEETKKLLLKAIVVDVEGTEAVEDEIEMLIENVKEDSMACGKILAERMIADGAKKILDEINLDRIK"},{"created_at":"2011-05-27T02:40:51.000Z","updated_at":"2011-05-27T15:01:18.000Z","name":"Uroporphyrinogen-III synthase","uniprot_id":"P06174","uniprot_name":"HEM4_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM4","num_residues":275,"molecular_weight":"30911.30078","theoretical_pi":"8.44","general_function":"Involved in uroporphyrinogen-III synthase activity","specific_function":"Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III","reactions":[{"id":2042,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2685,"direction":"\u003e","locations":null,"altext":"Hydroxymethylbilane = uroporphyrinogen III + H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"X89633","genbank_protein_id":"1279703","gene_card_id":"HEM4","chromosome_location":"chromosome 15","locus":"YOR278W","synonyms":["UROIIIS","UROS","Hydroxymethylbilane hydrolyase [cyclizing]","Uroporphyrinogen-III cosynthase"],"enzyme_classes":["4.2.1.75"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" uroporphyrinogen-III synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" biosynthetic process"},{"category":"Process","description":" cellular biosynthetic process"},{"category":"Process","description":" heterocycle biosynthetic process"},{"category":"Process","description":" tetrapyrrole biosynthetic process"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"HEM4","identifier":"PF02602"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGTCTAGTCGTAAAAAAGTCAGAGTATTACTGCTCAAGAATAAAACTGTCCCCATTGATAAATATGAATTGGAGTGTAGGAGTAAGGCGTTTGAACCCATATTCGTACCGCTTATTAAACATACACATGTAATTCAAGATTTTAGAAATGTTTTGAATACCATCCCAAACTATTTGAATACTATCAATTACATTATTATTACCTCTCAAAGGACTGTAGAGTCATTGAATGAAGCGATCATTCCCACATTGACAAGTGAACAAAAAGCTGCATTGCTCAGTAAAACAGTTTATACTGTAGGCCCTGCTACTGCTAACTTCATCAGAAGATCAGGTTTCATTAATGTTAAAGGTGGAGAAGACGCTGGTAATGGTTCAATCCTTGCTGATATAATTATTGATGACTTGAGTACGGATATTAAGGCATGCCCACCAAGTGAACTATTATTTCTCGTGGGTGAAATTAGAAGAGATATCATCCCAAAGAAACTCCATAGCAAGGGAATAAAAGTAAGAGAAGTGGTTACTTATAAAACTGAAGAATTAAGCGACGGTTTTAAAAGATTCATACACGCCATGAAAGAATGCGATGAGGATGAAGTATTCTCGGACTGGGTGGTAGTTTTCAGTCCCCAGGGAACGAAAGAAATTACTCAGTATTTGGGTGACAGTAACCGCCTACCAGGTTCCCATCTACGGGTTGCGTCCATCGGACCTACCACTAAAAAATATCTGGATGATAATGATGTAACCTCTGATGTGGTCAGTCCAAAACCGGACCCCAAGTCGCTATTAGATGCTATTGAATTATACCAGCGCCATAAATAA","protein_sequence":"MSSRKKVRVLLLKNKTVPIDKYELECRSKAFEPIFVPLIKHTHVIQDFRNVLNTIPNYLNTINYIIITSQRTVESLNEAIIPTLTSEQKAALLSKTVYTVGPATANFIRRSGFINVKGGEDAGNGSILADIIIDDLSTDIKACPPSELLFLVGEIRRDIIPKKLHSKGIKVREVVTYKTEELSDGFKRFIHAMKECDEDEVFSDWVVVFSPQGTKEITQYLGDSNRLPGSHLRVASIGPTTKKYLDDNDVTSDVVSPKPDPKSLLDAIELYQRHK"}]}