{"ymdb_id":"YMDB00910","created_at":"2011-05-29T19:04:07.000Z","updated_at":"2016-09-08T18:36:03.000Z","name":"IDP","cas":"86-04-4","state":"Solid","melting_point":"","description":"Inosine diphosphate (IDP) is an inosine nucleotide containing a pyrophosphate group esterified to C5 of the sugar moiety.","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"mitochondrion;cytoplasm","synthesis_reference":"Takada, Masao; Kashiwa, Kenichi.  Nucleoside 5'-pyrophosphates.    Jpn. Tokkyo Koho  (1971),     3 pp.  CODEN: JAXXAD  JP  46021587  19710618  Showa.   CAN 75:130076  AN 1971:530076    CAPLUS","chebi_id":"17808","hmdb_id":"HMDB03335","kegg_id":"C00104","pubchem_id":"644173","cs_id":"559208","foodb_id":null,"wikipedia_link":"IDP","biocyc_id":"IDP","iupac":"[({[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid","traditional_iupac":"{[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid","logp":"-3.588285764237081","pka":"3.3209774826690954","alogps_solubility":"4.26e+00 g/l","alogps_logp":"-0.99","alogps_logs":"-2.00","acceptor_count":"12","donor_count":"6","rotatable_bond_count":"6","polar_surface_area":"222.26","refractivity":"82.6442","polarizability":"33.7480237727735","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"1.7269501042007134","pka_strongest_acidic":"2.654971809008338","bioavailability":"0","number_of_rings":"3","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":["5'-IDP","IDP","Inosine 5'-(trihydrogen diphosphate)","Inosine 5'-(trihydrogen pyrophosphate)","Inosine 5'-diphosphate","Inosine 5'-pyrophosphate","Inosine diphosphate","Inosine pyrophosphate","Riboxine"],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"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":16330239,"citation":"Villarreal, J. M., Bueno, C., Arenas, F., Jabalquinto, A. M., Gonzalez-Nilo, F. D., Encinas, M. V., Cardemil, E. (2006). \"Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase Kinetics, fluorescence spectroscopy, and molecular simulation studies.\" Int J Biochem Cell Biol 38:576-588."}],"proteins":[{"created_at":"2011-05-26T16:57:01.000Z","updated_at":"2011-05-27T15:01:01.000Z","name":"Nucleoside diphosphate kinase","uniprot_id":"P36010","uniprot_name":"NDK_YEAST","enzyme":true,"transporter":false,"gene_name":"YNK1","num_residues":153,"molecular_weight":"17166.59961","theoretical_pi":"9.05","general_function":"Involved in nucleoside diphosphate kinase activity","specific_function":"Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage","reactions":[{"id":1786,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1787,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1788,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1789,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1790,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1791,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1792,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1793,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1794,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2454,"direction":"\u003e","locations":"Cytoplasm. Mitochondrion intermembrane space.","altext":"ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Mitochondrion intermembrane space.","genbank_gene_id":"AY558263","genbank_protein_id":"45270416","gene_card_id":"YNK1","chromosome_location":"chromosome 11","locus":"YKL067W","synonyms":["NDK","NDP kinase"],"enzyme_classes":["2.7.4.6"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" nucleoside diphosphate kinase activity"},{"category":"Process","description":" GTP biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" purine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" purine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" CTP biosynthetic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" pyrimidine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" UTP biosynthetic process"}],"pfams":[{"name":"NDK","identifier":"PF00334"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGTCTAGTCAAACAGAAAGAACTTTTATTGCGGTAAAACCAGATGGTGTCCAGAGGGGCTTAGTATCTCAAATTCTATCTCGTTTTGAAAAAAAAGGTTACAAACTAGTTGCTATTAAATTAGTTAAAGCGGATGATAAATTACTAGAGCAACATTACGCAGAGCATGTTGGTAAACCATTTTTCCCAAAGATGGTATCCTTTATGAAGTCTGGTCCCATTTTGGCCACGGTCTGGGAGGGAAAAGATGTGGTTAGACAAGGAAGAACTATTCTTGGTGCTACTAATCCTTTGGGCAGTGCACCAGGTACCATTAGAGGTGATTTCGGTATTGACCTAGGCAGAAACGTCTGTCACGGCAGTGATTCTGTTGATAGCGCTGAACGTGAAATCAATTTGTGGTTTAAGAAGGAAGAGTTAGTTGATTGGGAATCTAATCAAGCTAAGTGGATTTATGAATGA","protein_sequence":"MSSQTERTFIAVKPDGVQRGLVSQILSRFEKKGYKLVAIKLVKADDKLLEQHYAEHVGKPFFPKMVSFMKSGPILATVWEGKDVVRQGRTILGATNPLGSAPGTIRGDFGIDLGRNVCHGSDSVDSAEREINLWFKKEELVDWESNQAKWIYE"},{"created_at":"2011-05-26T18:45:56.000Z","updated_at":"2011-07-22T17:54:01.000Z","name":"Adenylate kinase 2","uniprot_id":"P26364","uniprot_name":"KAD2_YEAST","enzyme":true,"transporter":false,"gene_name":"ADK2","num_residues":225,"molecular_weight":"25193.69922","theoretical_pi":"9.42","general_function":"Involved in ATP binding","specific_function":"This small ubiquitous enzyme is essential for maintenance and cell growth","reactions":[{"id":1276,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1277,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1278,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2551,"direction":"\u003e","locations":"Cytoplasm. Nucleus;Cytoplasm, cytosol. Mitochondrion intermembrane space;Mitochondrion","altext":"ATP + AMP = 2 ADP.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"AY558457","genbank_protein_id":"45270804","gene_card_id":"ADK2","chromosome_location":"chromosome 5","locus":"YER170W","synonyms":["AK 2","ATP-AMP transphosphorylase 2"],"enzyme_classes":["2.7.4.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" kinase activity"},{"category":"Function","description":" nucleotide kinase activity"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" nucleobase, nucleoside, nucleotide kinase activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" adenylate kinase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"}],"pfams":[{"name":"ADK","identifier":"PF00406"},{"name":"ADK_lid","identifier":"PF05191"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"gene_sequence":"ATGAAAGCAGACGCGAAACAAATAACACATCTACTCAAACCTCTTCGACTTTTATTATTGGGGGCTCCAGGGTCAGGTAAAGGGACACAGACTTCGAGATTACTAAAGCAAATTCCACAATTATCTTCAATTTCGTCAGGCGACATTTTACGTCAGGAAATAAAATCTGAATCTACCCTAGGCCGAGAGGCTACTACCTACATTGCTCAAGGCAAGTTATTACCGGATGATCTCATAACGCGTCTGATAACTTTTCGTCTTTCGGCATTGGGTTGGTTAAAACCATCTGCCATGTGGTTGCTCGATGGATTTCCTCGAACTACTGCGCAAGCTTCTGCCTTAGACGAGCTGCTGAAACAGCATGACGCCAGCTTGAATCTAGTGGTAGAGCTAGATGTACCCGAATCCACCATATTAGAAAGGATCGAGAACAGATATGTTCACGTTCCTAGTGGGAGAGTGTATAACTTACAATATAATCCTCCCAAAGTGCCAGGATTAGACGATATCACCGGAGAACCATTGACCAAGAGGCTTGATGACACAGCGGAAGTGTTTAAAAAAAGGCTAGAAGAGTACAAGAAAACAAATGAGCCTTTAAAAGATTATTACAAAAAAAGTGGGATTTTTGGTACCGTCTCTGGGGAAACATCAGATATTATCTTCCGAAATTATTGA","protein_sequence":"MKADAKQITHLLKPLRLLLLGAPGSGKGTQTSRLLKQIPQLSSISSGDILRQEIKSESTLGREATTYIAQGKLLPDDLITRLITFRLSALGWLKPSAMWLLDGFPRTTAQASALDELLKQHDASLNLVVELDVPESTILERIENRYVHVPSGRVYNLQYNPPKVPGLDDITGEPLTKRLDDTAEVFKKRLEEYKKTNEPLKDYYKKSGIFGTVSGETSDIIFRNY"},{"created_at":"2011-05-26T18:59:10.000Z","updated_at":"2011-07-22T17:54:00.000Z","name":"Adenylate kinase 1","uniprot_id":"P07170","uniprot_name":"KAD1_YEAST","enzyme":true,"transporter":false,"gene_name":"ADK1","num_residues":222,"molecular_weight":"24254.5","theoretical_pi":"6.37","general_function":"Involved in ATP binding","specific_function":"Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Small ubiquitous enzyme involved in energy metabolism and nucleotide synthesis that is essential for maintenance and cell growth. Functions both in the cytoplasm and mitochondrion intermembrane space","reactions":[{"id":1276,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1277,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1278,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2551,"direction":"\u003e","locations":"Cytoplasm. Nucleus;Cytoplasm, cytosol. Mitochondrion intermembrane space;Mitochondrion","altext":"ATP + AMP = 2 ADP.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1AKY","cellular_location":"Cytoplasm, cytosol. Mitochondrion intermembrane space","genbank_gene_id":"AY558578","genbank_protein_id":"45271046","gene_card_id":"ADK1","chromosome_location":"chromosome 4","locus":"YDR226W","synonyms":["AK 1","ATP-AMP transphosphorylase 1","Adenylate kinase cytosolic and mitochondrial"],"enzyme_classes":["2.7.4.3"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" kinase activity"},{"category":"Function","description":" nucleotide kinase activity"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" nucleobase, nucleoside, nucleotide kinase activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" adenylate kinase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"}],"pfams":[{"name":"ADK","identifier":"PF00406"},{"name":"ADK_lid","identifier":"PF05191"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"}],"gene_sequence":"ATGTCTAGCTCAGAATCCATTAGAATGGTCCTAATTGGCCCACCTGGTGCCGGTAAAGGTACTCAAGCTCCAAATTTGCAAGAGCGTTTCCATGCCGCTCACTTGGCCACTGGTGACATGTTGAGATCTCAAATCGCAAAGGGCACTCAATTAGGTTTGGAAGCAAAGAAAATTATGGACCAAGGTGGTTTAGTCTCTGATGACATTATGGTTAACATGATCAAGGATGAATTGACCAACAATCCAGCTTGTAAGAATGGGTTCATCTTGGACGGTTTCCCAAAAACCATTCCTCAGGCTGAAAAATTGGACCAAATGTTGAAAGAACAAGGAACTCCTTTGGAAAAAGCCATCGAATTGAAGGTTGATGATGAATTGTTGGTTGCCAGAATTACCGGTAGATTAATTCACCCAGCCTCTGGCAGATCCTACCACAAGATCTTTAACCCACCAAAGGAAGACATGAAGGATGACGTCACCGGTGAAGCTTTAGTTCAAAGATCTGATGACAATGCAGACGCCTTGAAGAAGAGATTAGCTGCTTACCATGCTCAAACCGAACCAATTGTTGACTTTTACAAAAAGACCGGTATCTGGGCTGGTGTTGATGCTTCCCAACCTCCTGCTACTGTTTGGGCTGACATCTTGAACAAGCTAGGTAAGGATTAA","protein_sequence":"MSSSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILDGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQRSDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKD"}]}