{"ymdb_id":"YMDB00205","created_at":"2011-05-29T16:06:46.000Z","updated_at":"2016-09-08T18:35:10.000Z","name":"dTDP","cas":"491-97-4","state":"Solid","melting_point":null,"description":"Deoxythymidine diphosphate (dTDP) is a deoxyribonucleotide produced from dTMP. It is an ester of pyrophosphoric acid with the nucleoside thymidine. TDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase thymine. [Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":"Rupprath, Carsten; Kopp, Maren; Hirtz, Dennis; Mueller, Rolf; Elling, Lothar.  An enzyme module system for in situ regeneration of deoxythymidine 5'-diphosphate (dTDP)-activated deoxy sugars.    Advanced Synthesis \u0026 Catalysis  (2007),  349(8+9),  1489-149","chebi_id":"18075","hmdb_id":"HMDB01274","kegg_id":"C00363","pubchem_id":"164628","cs_id":"24604727","foodb_id":null,"wikipedia_link":"dTDP","biocyc_id":"TDP","iupac":"{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acid","traditional_iupac":"dTDP","logp":"-1.6644180996666658","pka":"3.210405220777684","alogps_solubility":"6.94e+00 g/l","alogps_logp":"-0.87","alogps_logs":"-1.76","acceptor_count":"9","donor_count":"5","rotatable_bond_count":"6","polar_surface_area":"192.15999999999997","refractivity":"77.1578","polarizability":"32.12109849726626","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.2403442590936775","pka_strongest_acidic":"1.7717480097137095","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["Deoxy-tdp","Deoxythymidine 5'-diphosphate","dTDP","TDP","Thymidine 5'-diphosphate","Thymidine 5'-pyrophosphate"],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"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."}],"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":" 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"},{"category":"Process","description":" GTP biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic 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"}],"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":"2011-05-26T21:15:58.000Z","updated_at":"2011-07-22T17:54:40.000Z","name":"Thymidylate kinase","uniprot_id":"P00572","uniprot_name":"KTHY_YEAST","enzyme":true,"transporter":false,"gene_name":"CDC8","num_residues":216,"molecular_weight":"24687.19922","theoretical_pi":"5.41","general_function":"Involved in thymidylate kinase activity","specific_function":"Catalyzes the conversion of dTMP to dTDP","reactions":[{"id":1474,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2607,"direction":"\u003e","locations":null,"altext":"ATP + dTMP = ADP + dTDP.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"3TMK","cellular_location":null,"genbank_gene_id":"K01783","genbank_protein_id":"171204","gene_card_id":"CDC8","chromosome_location":"chromosome 10","locus":"YJR057W","synonyms":["dTMP kinase"],"enzyme_classes":["2.7.4.9"],"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":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" thymidylate kinase activity"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleoside diphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" pyrimidine deoxyribonucleoside diphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" dTDP biosynthetic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"}],"pfams":[{"name":"Thymidylate_kin","identifier":"PF02223"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGATGGGTCGTGGCAAATTAATACTGATAGAAGGATTGGATAGGACTGGTAAAACCACGCAATGTAATATTCTTTACAAAAAATTGCAACCAAACTGTAAACTATTGAAGTTCCCCGAAAGGTCTACCCGAATCGGAGGACTCATAAACGAATATTTGACGGATGATACTTTCCAATTATCAGATCAGGCAATTCACCTCTTGTTTTCGGCAAATAGATGGGAAATAGTTGACAAGATAAAGAAAGATTTACTAGAAGGCAAGAACATTGTCATGGACAGATATGTTTATTCTGGAGTGGCATATTCTGCCGCTAAGGGGACAAATGGAATGGATTTGGATTGGTGCTTGCAACCCGATGTAGGGTTGCTGAAACCGGATTTGACATTATTTTTAAGCACTCAAGATGTCGACAATAACGCCGAAAAATCTGGATTTGGTGACGAAAGATACGAAACTGTTAAGTTTCAAGAAAAAGTGAAGCAAACTTTTATGAAGCTATTGGATAAAGAGATAAGGAAAGGCGATGAGTCAATCACGATTGTAGACGTTACTAATAAGGGCATTCAGGAAGTTGAAGCGCTTATTTGGCAAATCGTTGAGCCTGTTTTGAGTACGCATATTGATCATGATAAATTTTCGTTCTTCTAG","protein_sequence":"MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF"}]}