{"ymdb_id":"YMDB00390","created_at":"2011-05-29T18:12:07.000Z","updated_at":"2016-09-08T18:35:26.000Z","name":"3-Dehydroshikimic acid","cas":"27655-56-7","state":null,"melting_point":null,"description":"3-Dehydroshikimic acid is an intermediate in the chorismate biosynthesis pathway also called shikimate pathway. This pathway occurs in plants and microorganisms. Chorismate is an important intermediate that leads to the biosynthesis of several essential metabolites, including the aromatic amino acids L-phenylalanine, L-tyrosine and L-tryptophan, vitamins E and K, ubiquinone and certain siderophore. [Biocyc ARO-PWY] ","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Cytoplasm","synthesis_reference":null,"chebi_id":"30918","hmdb_id":null,"kegg_id":"C02637","pubchem_id":"439774","cs_id":"388830","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"(4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid","traditional_iupac":"3-dehydroshikimic acid","logp":"-1.024897902666667","pka":"12.41661028782423","alogps_solubility":"1.37e+02 g/l","alogps_logp":"-1.19","alogps_logs":"-0.10","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"1","polar_surface_area":"94.83","refractivity":"38.1936","polarizability":"14.914686507045417","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"-3.2670456083440538","pka_strongest_acidic":"3.2142420075706486","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(-)-3-dehydroshikimic acid","3-Dehydroshikimate","3-dehydroshikimic acid","5-Dehydroshikimate","5-dehydroshikimic acid"],"pathways":[{"name":"Phenylalanine, tyrosine and tryptophan biosynthesis","kegg_map_id":"00400"}],"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":6355828,"citation":"Larimer, F. W., Morse, C. C., Beck, A. K., Cole, K. W., Gaertner, F. H. (1983). \"Isolation of the ARO1 cluster gene of Saccharomyces cerevisiae.\" Mol Cell Biol 3:1609-1614."}],"proteins":[{"created_at":"2011-05-24T20:47:22.000Z","updated_at":"2011-07-22T17:53:48.000Z","name":"Pentafunctional AROM polypeptide","uniprot_id":"P08566","uniprot_name":"ARO1_YEAST","enzyme":true,"transporter":false,"gene_name":"ARO1","num_residues":1588,"molecular_weight":"174754.0","theoretical_pi":"6.22","general_function":"Involved in 3-dehydroquinate dehydratase activity","specific_function":"The AROM polypeptide catalyzes 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis","reactions":[{"id":1162,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1163,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1187,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1965,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1966,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2343,"direction":"\u003e","locations":"Cytoplasm","altext":"3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":2344,"direction":"\u003e","locations":"Cytoplasm","altext":"3-dehydroquinate = 3-dehydroshikimate + H(2)O.","export":false,"pw_reaction_id":null,"source":null},{"id":2345,"direction":"\u003e","locations":"Cytoplasm","altext":"Shikimate + NADP(+) = 3-dehydroshikimate + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":2346,"direction":"\u003e","locations":"Cytoplasm","altext":"ATP + shikimate = ADP + shikimate 3-phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":2347,"direction":"\u003e","locations":"Cytoplasm","altext":"Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O-(1-carboxyvinyl)-3-phosphoshikimate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"X06077","genbank_protein_id":"3381","gene_card_id":"ARO1","chromosome_location":"chromosome 4","locus":"YDR127W","synonyms":["3-dehydroquinate synthase","3-phosphoshikimate 1-carboxyvinyltransferase","5-enolpyruvylshikimate-3-phosphate synthase","EPSP synthase","EPSPS","Shikimate kinase","3-dehydroquinate dehydratase","3-dehydroquinase","Shikimate dehydrogenase"],"enzyme_classes":["4.2.3.4","2.5.1.19","2.7.1.71","4.2.1.10","1.1.1.25"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" 3-dehydroquinate dehydratase activity"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" kinase activity"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" shikimate kinase activity"},{"category":"Function","description":" shikimate 5-dehydrogenase activity"},{"category":"Function","description":" transferase activity, transferring alkyl or aryl (other than methyl) groups"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" 3-phosphoshikimate 1-carboxyvinyltransferase activity"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" carbon-oxygen lyase activity, acting on phosphates"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" 3-dehydroquinate synthase activity"},{"category":"Process","description":" aromatic amino acid family biosynthetic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular amino acid biosynthetic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"DHQ_synthase","identifier":"PF01761"},{"name":"DHquinase_I","identifier":"PF01487"},{"name":"EPSP_synthase","identifier":"PF00275"},{"name":"Shikimate_DH","identifier":"PF01488"},{"name":"Shikimate_dh_N","identifier":"PF08501"},{"name":"SKI","identifier":"PF01202"}],"pathways":[{"name":"Phenylalanine, tyrosine and tryptophan biosynthesis","kegg_map_id":"00400"}],"gene_sequence":"ATGGTGCAGTTAGCCAAAGTCCCAATTCTAGGAAATGATATTATCCACGTTGGGTATAACATTCATGACCATTTGGTTGAAACCATAATTAAACATTGTCCTTCTTCGACATACGTTATTTGCAATGATACGAACTTGAGTAAAGTTCCATACTACCAGCAATTAGTCCTGGAATTCAAGGCTTCTTTGCCAGAAGGCTCTCGTTTACTTACTTATGTTGTTAAACCAGGTGAGACAAGTAAAAGTAGAGAAACCAAAGCGCAGCTAGAAGATTATCTTTTAGTGGAAGGATGTACTCGTGATACGGTTATGGTAGCGATCGGTGGTGGTGTTATTGGTGACATGATTGGGTTCGTTGCATCTACATTTATGAGAGGTGTTCGTGTTGTCCAAGTACCAACATCCTTATTGGCAATGGTCGATTCCTCCATTGGTGGTAAAACTGCTATTGACACTCCTCTAGGTAAAAACTTTATTGGTGCATTTTGGCAACCAAAATTTGTCCTTGTAGATATTAAATGGCTAGAAACGTTAGCCAAGAGAGAGTTTATCAATGGGATGGCAGAAGTTATCAAGACTGCTTGTATTTGGAACGCTGACGAATTTACTAGATTAGAATCAAACGCTTCGTTGTTCTTAAATGTTGTTAATGGGGCAAAAAATGTCAAGGTTACCAATCAATTGACAAACGAGATTGACGAGATATCGAATACAGATATTGAAGCTATGTTGGATCATACATATAAGTTAGTTCTTGAGAGTATTAAGGTCAAAGCGGAAGTTGTCTCTTCGGATGAACGTGAATCCAGTCTAAGAAACCTTTTGAACTTCGGACATTCTATTGGTCATGCTTATGAAGCTATACTAACCCCACAAGCATTACATGGTGAATGTGTGTCCATTGGTATGGTTAAAGAGGCGGAATTATCCCGTTATTTCGGTATTCTCTCCCCTACCCAAGTTGCACGTCTATCCAAGATTTTGGTTGCCTACGGGTTGCCTGTTTCGCCTGATGAGAAATGGTTTAAAGAGCTAACCTTACATAAGAAAACACCATTGGATATCTTATTGAAGAAAATGAGTATTGACAAGAAAAACGAGGGTTCCAAAAAGAAGGTGGTCATTTTAGAAAGTATTGGTAAGTGCTATGGTGACTCCGCTCAATTTGTTAGCGATGAAGACCTGAGATTTATTCTAACAGATGAAACCCTCGTTTACCCCTTCAAGGACATCCCTGCTGATCAACAGAAAGTTGTTATCCCCCCTGGTTCTAAGTCCATCTCCAATCGTGCTTTAATTCTTGCTGCCCTCGGTGAAGGTCAATGTAAAATCAAGAACTTATTACATTCTGATGATACTAAACATATGTTAACCGCTGTTCATGAATTGAAAGGTGCTACGATATCATGGGAAGATAATGGTGAGACGGTAGTGGTGGAAGGACATGGTGGTTCCACATTGTCAGCTTGTGCTGACCCCTTATATCTAGGTAATGCAGGTACTGCATCTAGATTTTTGACTTCCTTGGCTGCCTTGGTCAATTCTACTTCAAGCCAAAAGTATATCGTTTTAACTGGTAACGCAAGAATGCAACAAAGACCAATTGCTCCTTTGGTCGATTCTTTGCGTGCTAATGGTACTAAAATTGAGTACTTGAATAATGAAGGTTCCCTGCCAATCAAAGTTTATACTGATTCGGTATTCAAAGGTGGTAGAATTGAATTAGCTGCTACAGTTTCTTCTCAGTACGTATCCTCTATCTTGATGTGTGCCCCATACGCTGAAGAACCTGTAACTTTGGCTCTTGTTGGTGGTAAGCCAATCTCTAAATTGTACGTCGATATGACAATAAAAATGATGGAAAAATTCGGTATCAATGTTGAAACTTCTACTACAGAACCTTACACTTATTATATTCCAAAGGGACATTATATTAACCCATCAGAATACGTCATTGAAAGTGATGCCTCAAGTGCTACATACCCATTGGCCTTCGCCGCAATGACTGGTACTACCGTAACGGTTCCAAACATTGGTTTTGAGTCGTTACAAGGTGATGCCAGATTTGCAAGAGATGTCTTGAAACCTATGGGTTGTAAAATAACTCAAACGGCAACTTCAACTACTGTTTCGGGTCCTCCTGTAGGTACTTTAAAGCCATTAAAACATGTTGATATGGAGCCAATGACTGATGCGTTCTTAACTGCATGTGTTGTTGCCGCTATTTCGCACGACAGTGATCCAAATTCTGCAAATACAACCACCATTGAAGGTATTGCAAACCAGCGTGTCAAAGAGTGTAACAGAATTTTGGCCATGGCTACAGAGCTCGCCAAATTTGGCGTCAAAACTACAGAATTACCAGATGGTATTCAAGTCCATGGTTTAAACTCGATAAAAGATTTGAAGGTTCCTTCCGACTCTTCTGGACCTGTCGGTGTATGCACATATGATGATCATCGTGTGGCCATGAGTTTCTCGCTTCTTGCAGGAATGGTAAATTCTCAAAATGAACGTGACGAAGTTGCTAATCCTGTAAGAATACTTGAAAGACATTGTACTGGTAAAACCTGGCCTGGCTGGTGGGATGTGTTACATTCCGAACTAGGTGCCAAATTAGATGGTGCAGAACCTTTAGAGTGCACATCCAAAAAGAACTCAAAGAAAAGCGTTGTCATTATTGGCATGAGAGCAGCTGGCAAAACTACTATAAGTAAATGGTGCGCATCCGCTCTGGGTTACAAATTAGTTGACCTAGACGAGCTGTTTGAGCAACAGCATAACAATCAAAGTGTTAAACAATTTGTTGTGGAGAACGGTTGGGAGAAGTTCCGTGAGGAAGAAACAAGAATTTTCAAGGAAGTTATTCAAAATTACGGCGATGATGGATATGTTTTCTCAACAGGTGGCGGTATTGTTGAAAGCGCTGAGTCTAGAAAAGCCTTAAAAGATTTTGCCTCATCAGGTGGATACGTTTTACACTTACATAGGGATATTGAGGAGACAATTGTCTTTTTACAAAGTGATCCTTCAAGACCTGCCTATGTGGAAGAAATTCGTGAAGTTTGGAACAGAAGGGAGGGGTGGTATAAAGAATGCTCAAATTTCTCTTTCTTTGCTCCTCATTGCTCCGCAGAAGCTGAGTTCCAAGCTCTAAGAAGATCGTTTAGTAAGTACATTGCAACCATTACAGGTGTCAGAGAAATAGAAATTCCAAGCGGAAGATCTGCCTTTGTGTGTTTAACCTTTGATGACTTAACTGAACAAACTGAGAATTTGACTCCAATCTGTTATGGTTGTGAGGCTGTAGAGGTCAGAGTAGACCATTTGGCTAATTACTCTGCTGATTTCGTGAGTAAACAGTTATCTATATTGCGTAAAGCCACTGACAGTATTCCTATCATTTTTACTGTGCGAACCATGAAGCAAGGTGGCAACTTTCCTGATGAAGAGTTCAAAACCTTGAGAGAGCTATACGATATTGCCTTGAAGAATGGTGTTGAATTCCTTGACTTAGAACTAACTTTACCTACTGATATCCAATATGAGGTTATTAACAAAAGGGGCAACACCAAGATCATTGGTTCCCATCATGACTTCCAAGGATTATACTCCTGGGACGACGCTGAATGGGAAAACAGATTCAATCAAGCGTTAACTCTTGATGTGGATGTTGTAAAATTTGTGGGTACGGCTGTTAATTTCGAAGATAATTTGAGACTGGAACACTTTAGGGATACACACAAGAATAAGCCTTTAATTGCAGTTAATATGACTTCTAAAGGTAGCATTTCTCGTGTTTTGAATAATGTTTTAACACCTGTGACATCAGATTTATTGCCTAACTCCGCTGCCCCTGGCCAATTGACAGTAGCACAAATTAACAAGATGTATACATCTATGGGAGGTATCGAGCCTAAGGAACTGTTTGTTGTTGGAAAGCCAATTGGCCACTCTAGATCGCCAATTTTACATAACACTGGCTATGAAATTTTAGGTTTACCTCACAAGTTCGATAAATTTGAAACTGAATCCGCACAATTGGTGAAAGAAAAACTTTTGGACGGAAACAAGAACTTTGGCGGTGCTGCAGTCACAATTCCTCTGAAATTAGATATAATGCAGTACATGGATGAATTGACTGATGCTGCTAAAGTTATTGGTGCTGTAAACACAGTTATACCATTGGGTAACAAGAAGTTTAAGGGTGATAATACCGACTGGTTAGGTATCCGTAATGCCTTAATTAACAATGGCGTTCCCGAATATGTTGGTCATACCGCTGGTTTGGTTATCGGTGCAGGTGGCACTTCTAGAGCCGCCCTTTACGCCTTGCACAGTTTAGGTTGCAAAAAGATCTTCATAATCAACAGGACAACTTCGAAATTGAAGCCATTAATAGAGTCACTTCCATCTGAATTCAACATTATTGGAATAGAGTCCACTAAATCTATAGAAGAGATTAAGGAACACGTTGGCGTTGCTGTCAGCTGTGTACCAGCCGACAAACCATTAGATGACGAACTTTTAAGTAAGCTGGAGAGATTCCTTGTGAAAGGTGCCCATGCTGCTTTTGTACCAACCTTATTGGAAGCCGCATACAAACCAAGCGTTACTCCCGTTATGACAATTTCACAAGACAAATATCAATGGCACGTTGTCCCTGGATCACAAATGTTAGTACACCAAGGTGTAGCTCAGTTTGAAAAGTGGACAGGATTCAAGGGCCCTTTCAAGGCCATTTTTGATGCCGTTACGAAAGAGTAG","protein_sequence":"MVQLAKVPILGNDIIHVGYNIHDHLVETIIKHCPSSTYVICNDTNLSKVPYYQQLVLEFKASLPEGSRLLTYVVKPGETSKSRETKAQLEDYLLVEGCTRDTVMVAIGGGVIGDMIGFVASTFMRGVRVVQVPTSLLAMVDSSIGGKTAIDTPLGKNFIGAFWQPKFVLVDIKWLETLAKREFINGMAEVIKTACIWNADEFTRLESNASLFLNVVNGAKNVKVTNQLTNEIDEISNTDIEAMLDHTYKLVLESIKVKAEVVSSDERESSLRNLLNFGHSIGHAYEAILTPQALHGECVSIGMVKEAELSRYFGILSPTQVARLSKILVAYGLPVSPDEKWFKELTLHKKTPLDILLKKMSIDKKNEGSKKKVVILESIGKCYGDSAQFVSDEDLRFILTDETLVYPFKDIPADQQKVVIPPGSKSISNRALILAALGEGQCKIKNLLHSDDTKHMLTAVHELKGATISWEDNGETVVVEGHGGSTLSACADPLYLGNAGTASRFLTSLAALVNSTSSQKYIVLTGNARMQQRPIAPLVDSLRANGTKIEYLNNEGSLPIKVYTDSVFKGGRIELAATVSSQYVSSILMCAPYAEEPVTLALVGGKPISKLYVDMTIKMMEKFGINVETSTTEPYTYYIPKGHYINPSEYVIESDASSATYPLAFAAMTGTTVTVPNIGFESLQGDARFARDVLKPMGCKITQTATSTTVSGPPVGTLKPLKHVDMEPMTDAFLTACVVAAISHDSDPNSANTTTIEGIANQRVKECNRILAMATELAKFGVKTTELPDGIQVHGLNSIKDLKVPSDSSGPVGVCTYDDHRVAMSFSLLAGMVNSQNERDEVANPVRILERHCTGKTWPGWWDVLHSELGAKLDGAEPLECTSKKNSKKSVVIIGMRAAGKTTISKWCASALGYKLVDLDELFEQQHNNQSVKQFVVENGWEKFREEETRIFKEVIQNYGDDGYVFSTGGGIVESAESRKALKDFASSGGYVLHLHRDIEETIVFLQSDPSRPAYVEEIREVWNRREGWYKECSNFSFFAPHCSAEAEFQALRRSFSKYIATITGVREIEIPSGRSAFVCLTFDDLTEQTENLTPICYGCEAVEVRVDHLANYSADFVSKQLSILRKATDSIPIIFTVRTMKQGGNFPDEEFKTLRELYDIALKNGVEFLDLELTLPTDIQYEVINKRGNTKIIGSHHDFQGLYSWDDAEWENRFNQALTLDVDVVKFVGTAVNFEDNLRLEHFRDTHKNKPLIAVNMTSKGSISRVLNNVLTPVTSDLLPNSAAPGQLTVAQINKMYTSMGGIEPKELFVVGKPIGHSRSPILHNTGYEILGLPHKFDKFETESAQLVKEKLLDGNKNFGGAAVTIPLKLDIMQYMDELTDAAKVIGAVNTVIPLGNKKFKGDNTDWLGIRNALINNGVPEYVGHTAGLVIGAGGTSRAALYALHSLGCKKIFIINRTTSKLKPLIESLPSEFNIIGIESTKSIEEIKEHVGVAVSCVPADKPLDDELLSKLERFLVKGAHAAFVPTLLEAAYKPSVTPVMTISQDKYQWHVVPGSQMLVHQGVAQFEKWTGFKGPFKAIFDAVTKE"}]}