{"ymdb_id":"YMDB00987","created_at":"2011-06-14T19:23:38.000Z","updated_at":"2016-09-08T18:36:07.000Z","name":"Protoheme IX","cas":"14875-96-8","state":"Solid","melting_point":null,"description":"Protoheme IX (heme b or heme) is the final product in the heme biosynthesis from uroporphyrinogen-III pathway. It is an iron-containing prosthetic group found in many essential proteins including cytochromes and heme-containing globins. In addition to its role in oxidative metabolism, heme also functions as a regulatory molecule in transcription, translation, protein targeting, protein stability, and cellular differentiation. Different derivatives of protoheme can actually be formed that differ in modifications to the porphyrin ring, including how it is bound to the protein (e.g. heme o, heme a, heme c, and heme d). [Biocyc PWY-5189]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":"17627","hmdb_id":"HMDB03178","kegg_id":"C00032","pubchem_id":"26945","cs_id":"21864835","foodb_id":null,"wikipedia_link":"Heme_b","biocyc_id":"PROTOHEME","iupac":"3-[(12Z)-20-(2-carboxyethyl)-10,15-diethenyl-5,9,14,19-tetramethyl-21,23,24,25-tetraaza-22-ferrahexacyclo[9.9.3.1³,⁶.1¹³,¹⁶.0⁸,²³.0¹⁸,²¹]pentacosa-1,3(25),4,6,8,10,12,14,16(24),17,19-undecaen-4-yl]propanoic acid","traditional_iupac":"3-[(12Z)-20-(2-carboxyethyl)-10,15-diethenyl-5,9,14,19-tetramethyl-21,23,24,25-tetraaza-22-ferrahexacyclo[9.9.3.1³,⁶.1¹³,¹⁶.0⁸,²³.0¹⁸,²¹]pentacosa-1,3(25),4,6,8,10,12,14,16(24),17,19-undecaen-4-yl]propanoic acid","logp":"8.067757694939885","pka":"4.224056667739481","alogps_solubility":"6.24e-02 g/l","alogps_logp":"4.06","alogps_logs":"-3.99","acceptor_count":"6","donor_count":"2","rotatable_bond_count":"8","polar_surface_area":"110.24000000000001","refractivity":"165.0326","polarizability":"67.51726584040702","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"2.8450848259624517","pka_strongest_acidic":"3.6557588220715034","bioavailability":"0","number_of_rings":"6","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["(protoporphyrinato)iron","[3,7,12,17-tetramethyl-8,13-divinylporphyrin-2,18-dipropanoato(2-)]iron(II)","[Fe(ppIX)]","Fe(ppIX)","Ferroheme","Ferroheme b","Ferroprotoheme","Ferroprotoporphyrin","Ferroprotoporphyrin IX","Ferrous protoheme","Ferrous protoheme IX","haem","Hem","heme","heme b","hemeb","Iron protoporphyrin","Iron protoporphyrin IX","Iron(II) protoporphyrin IX","Protoferroheme","Protohaem","Protoheme","Protoheme IX","Protoheme IX (VAN)","Reduced hematin"],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"},{"name":"Oxidative phosphorylation","kegg_map_id":"00190"},{"name":"Porphyrin Metabolism","kegg_map_id":null},{"name":"Steroid biosynthesis","kegg_map_id":"00100"}],"growth_conditions":[],"references":[{"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":8818224,"citation":"Gora, M., Chacinska, A., Rytka, J., Labbe-Bois, R. (1996). \"Isolation and functional characterization of mutant ferrochelatases in Saccharomyces cerevisiae.\" Biochimie 78:144-152."},{"pubmed_id":6753940,"citation":"Camadro, J. M., Labbe, P. (1982). \"Kinetic studies of ferrochelatase in yeast. Zinc or iron as competing substrates.\" Biochim Biophys Acta 707:280-288."}],"proteins":[{"created_at":"2011-05-24T21:11:28.000Z","updated_at":"2011-07-22T17:55:05.000Z","name":"Ferrochelatase, mitochondrial","uniprot_id":"P16622","uniprot_name":"HEMH_YEAST","enzyme":true,"transporter":false,"gene_name":"HEM15","num_residues":393,"molecular_weight":"44595.80078","theoretical_pi":"9.46","general_function":"Involved in ferrochelatase activity","specific_function":"Catalyzes the ferrous insertion into protoporphyrin IX","reactions":[{"id":1538,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2366,"direction":"\u003e","locations":"Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.","altext":"Protoheme + 2 H(+) = protoporphyrin + Fe(2+).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1LBQ","cellular_location":"Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.","genbank_gene_id":"J05395","genbank_protein_id":"171660","gene_card_id":"HEM15","chromosome_location":"chromosome 15","locus":"YOR176W","synonyms":["Heme synthase","Protoheme ferro-lyase"],"enzyme_classes":["4.99.1.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" ferrochelatase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" heme biosynthetic process"},{"category":"Process","description":" tetrapyrrole metabolic process"},{"category":"Process","description":" porphyrin metabolic process"},{"category":"Process","description":" porphyrin biosynthetic process"}],"pfams":[{"name":"Ferrochelatase","identifier":"PF00762"}],"pathways":[{"name":"Porphyrin and chlorophyll metabolism","kegg_map_id":"00860"}],"gene_sequence":"ATGCTTTCCAGAACAATCCGTACACAAGGTTCCTTCCTAAGAAGATCACAACTGACCATTACAAGATCATTTTCGGTTACATTCAACATGCAGAATGCACAAAAGAGATCACCCACAGGAATTGTTTTGATGAACATGGGTGGCCCCTCTAAAGTTGAGGAAACATATGATTTTTTGTATCAATTATTTGCCGATAATGACCTAATTCCCATTAGTGCTAAGTATCAGAAGACAATTGCTAAATATATTGCTAAGTTTCGTACCCCCAAGATAGAGAAGCAATATAGGGAAATTGGTGGGGGCTCCCCAATCCGGAAATGGTCTGAGTATCAAGCCACTGAGGTCTGTAAAATCTTAGATAAAACCTGTCCAGAAACGGCGCCTCATAAGCCTTACGTGGCGTTTCGTTACGCAAAGCCGCTAACCGCAGAAACTTATAAACAAATGCTAAAAGATGGCGTGAAGAAGGCAGTGGCCTTTTCTCAATATCCTCATTTCTCTTATTCCACTACCGGGTCATCCATCAACGAATTGTGGAGACAGATTAAGGCATTGGACTCCGAGAGATCTATATCTTGGTCGGTTATTGATCGTTGGCCTACAAATGAAGGTCTAATCAAGGCCTTCTCCGAAAATATCACCAAAAAACTACAAGAGTTTCCGCAACCTGTCAGAGACAAGGTTGTTTTATTGTTTTCCGCACATTCTCTACCCATGGATGTTGTTAACACCGGTGATGCCTACCCAGCTGAGGTAGCTGCGACGGTTTACAACATCATGCAAAAATTAAAGTTTAAAAACCCTTATAGGTTGGTTTGGCAATCCCAAGTTGGACCAAAACCATGGTTGGGAGCGCAGACAGCTGAAATTGCGGAATTTTTAGGCCCCAAAGTTGATGGCCTAATGTTTATTCCTATCGCCTTTACCTCTGATCATATTGAAACATTGCATGAAATTGACTTAGGCGTCATTGGGGAATCGGAATATAAGGATAAATTTAAGAGATGCGAATCTTTAAATGGCAACCAGACCTTTATTGAAGGCATGGCAGATCTCGTCAAAAGCCACTTACAGAGTAACCAACTCTATTCTAATCAACTACCTCTTGATTTTGCACTTGGCAAGTCCAATGATCCTGTAAAGGACCTTTCATTGGTATTTGGCAATCACGAATCTACTTGA","protein_sequence":"MLSRTIRTQGSFLRRSQLTITRSFSVTFNMQNAQKRSPTGIVLMNMGGPSKVEETYDFLYQLFADNDLIPISAKYQKTIAKYIAKFRTPKIEKQYREIGGGSPIRKWSEYQATEVCKILDKTCPETAPHKPYVAFRYAKPLTAETYKQMLKDGVKKAVAFSQYPHFSYSTTGSSINELWRQIKALDSERSISWSVIDRWPTNEGLIKAFSENITKKLQEFPQPVRDKVVLLFSAHSLPMDVVNTGDAYPAEVAATVYNIMQKLKFKNPYRLVWQSQVGPKPWLGAQTAEIAEFLGPKVDGLMFIPIAFTSDHIETLHEIDLGVIGESEYKDKFKRCESLNGNQTFIEGMADLVKSHLQSNQLYSNQLPLDFALGKSNDPVKDLSLVFGNHEST"}]}