{"ymdb_id":"YMDB00670","created_at":"2011-05-29T18:42:06.000Z","updated_at":"2016-09-08T18:35:45.000Z","name":"geranyl diphosphate","cas":"763-10-0","state":"Solid","melting_point":null,"description":"Geranyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of farnesyl pyrophosphate, geranylgeranyl pyrophosphate, cholesterol, terpenes and terpenoids.[Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Cytoplasm","synthesis_reference":null,"chebi_id":"17211","hmdb_id":"HMDB01285","kegg_id":"C00341","pubchem_id":"445995","cs_id":"24785181","foodb_id":null,"wikipedia_link":"Geranyl_pyrophosphate","biocyc_id":"GERANYL-PP","iupac":"[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid","traditional_iupac":"geranyl diphosphate","logp":"1.9570187856666668","pka":"3.2043406094078315","alogps_solubility":"9.02e-01 g/l","alogps_logp":"1.63","alogps_logs":"-2.54","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"8","polar_surface_area":"113.29000000000002","refractivity":"72.92789999999998","polarizability":"28.51754860324528","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":null,"pka_strongest_acidic":"1.7672186885241006","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"1","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate","Geranyl diphosphate","geranyl pyrophosphate","Geranyl pyrophosphic acid","geranyl-diphosphate","geranyl-PP","geranyl-pyrophosphate","Monoterpenyl diphosphate","Neryl diphosphate","trans-geranyl pyrophosphate"],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Ubiquinone and other terpenoid-quinone biosynthesis","kegg_map_id":"00130"},{"name":"Steroid biosynthesis","kegg_map_id":"00100"},{"name":"Cholesterol biosynthesis and metabolism CE(14:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(10:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(12:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(16:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(18:0)","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":12702274,"citation":"Grabinska, K., Palamarczyk, G. (2002). \"Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase.\" FEMS Yeast Res 2:259-265."},{"pubmed_id":16484724,"citation":"Song, L. (2006). \"A soluble form of phosphatase in Saccharomyces cerevisiae capable of converting farnesyl diphosphate into E,E-farnesol.\" Appl Biochem Biotechnol 128:149-158."}],"proteins":[{"created_at":"2011-05-26T18:23:18.000Z","updated_at":"2011-07-22T17:54:38.000Z","name":"Farnesyl pyrophosphate synthase","uniprot_id":"P08524","uniprot_name":"FPPS_YEAST","enzyme":true,"transporter":false,"gene_name":"ERG20","num_residues":352,"molecular_weight":"40483.0","theoretical_pi":"5.11","general_function":"Involved in isoprenoid biosynthetic process","specific_function":"Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate","reactions":[{"id":1466,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1562,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2529,"direction":"\u003e","locations":"Cytoplasm","altext":"Dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":2530,"direction":"\u003e","locations":"Cytoplasm","altext":"Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14374,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006891","source":"Smpdb"},{"id":14375,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006892","source":"Smpdb"},{"id":14376,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R007264","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"J05091","genbank_protein_id":"171517","gene_card_id":"ERG20","chromosome_location":"chromosome 10","locus":"YJL167W","synonyms":["FPP synthase","FPS","Farnesyl diphosphate synthase","Dimethylallyltranstransferase","Geranyltranstransferase"],"enzyme_classes":["2.5.1.10","2.5.1.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" Not Available"},{"category":"Process","description":" isoprenoid metabolic process"},{"category":"Process","description":" isoprenoid biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" primary metabolic process"},{"category":"Process","description":" lipid metabolic process"},{"category":"Process","description":" cellular lipid metabolic process"}],"pfams":[{"name":"polyprenyl_synt","identifier":"PF00348"}],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Cholesterol biosynthesis and metabolism CE(10:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(12:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(14:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(16:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(18:0)","kegg_map_id":null}],"gene_sequence":"ATGGCTTCAGAAAAAGAAATTAGGAGAGAGAGATTCTTGAACGTTTTCCCTAAATTAGTAGAGGAATTGAACGCATCGCTTTTGGCTTACGGTATGCCTAAGGAAGCATGTGACTGGTATGCCCACTCATTGAACTACAACACTCCAGGCGGTAAGCTAAATAGAGGTTTGTCCGTTGTGGACACGTATGCTATTCTCTCCAACAAGACCGTTGAACAATTGGGGCAAGAAGAATACGAAAAGGTTGCCATTCTAGGTTGGTGCATTGAGTTGTTGCAGGCTTACTTCTTGGTCGCCGATGATATGATGGACAAGTCCATTACCAGAAGAGGCCAACCATGTTGGTACAAGGTTCCTGAAGTTGGGGAAATTGCCATCAATGACGCATTCATGTTAGAGGCTGCTATCTACAAGCTTTTGAAATCTCACTTCAGAAACGAAAAATACTACATAGATATCACCGAATTGTTCCATGAGGTCACCTTCCAAACCGAATTGGGCCAATTGATGGACTTAATCACTGCACCTGAAGACAAAGTCGACTTGAGTAAGTTCTCCCTAAAGAAGCACTCCTTCATAGTTACTTTCAAGACTGCTTACTATTCTTTCTACTTGCCTGTCGCATTGGCCATGTACGTTGCCGGTATCACGGATGAAAAGGATTTGAAACAAGCCAGAGATGTCTTGATTCCATTGGGTGAATACTTCCAAATTCAAGATGACTACTTAGACTGCTTCGGTACCCCAGAACAGATCGGTAAGATCGGTACAGATATCCAAGATAACAAATGTTCTTGGGTAATCAACAAGGCATTGGAACTTGCTTCCGCAGAACAAAGAAAGACTTTAGACGAAAATTACGGTAAGAAGGACTCAGTCGCAGAAGCCAAATGCAAAAAGATTTTCAATGACTTGAAAATTGAACAGCTATACCACGAATATGAAGAGTCTATTGCCAAGGATTTGAAGGCCAAAATTTCTCAGGTCGATGAGTCTCGTGGCTTCAAAGCTGATGTCTTAACTGCGTTCTTGAACAAAGTTTACAAGAGAAGCAAATAG","protein_sequence":"MASEKEIRRERFLNVFPKLVEELNASLLAYGMPKEACDWYAHSLNYNTPGGKLNRGLSVVDTYAILSNKTVEQLGQEEYEKVAILGWCIELLQAYFLVADDMMDKSITRRGQPCWYKVPEVGEIAINDAFMLEAAIYKLLKSHFRNEKYYIDITELFHEVTFQTELGQLMDLITAPEDKVDLSKFSLKKHSFIVTFKTAYYSFYLPVALAMYVAGITDEKDLKQARDVLIPLGEYFQIQDDYLDCFGTPEQIGKIGTDIQDNKCSWVINKALELASAEQRKTLDENYGKKDSVAEAKCKKIFNDLKIEQLYHEYEESIAKDLKAKISQVDESRGFKADVLTAFLNKVYKRSK"}]}