{"ymdb_id":"YMDB00745","created_at":"2011-05-29T18:49:17.000Z","updated_at":"2016-10-18T17:11:35.000Z","name":"dTTP","cas":"365-08-2","state":"Solid","melting_point":null,"description":"Deoxythymidine triphosphate (dTTP) is one of the five nucleoside triphosphates that are used in the in vivo synthesis of DNA. DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides having the bases: adenine, cytosine, guanine, and thymine. A nucleotide is a mono-, di-, or triphosphate deoxyribonucleoside; that is, a deoxyribose sugar is attached to one, two, or three phosphates. Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine, and cytosine pairs with guanine. [Wikipedia]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"extracellular;cytoplasm","synthesis_reference":"Ikehara, Morio; Ohtsuka, Eiko. Coenzyme analogs. XXI. A new synthesis of thymidine 5'-triphosphate and the use of P1,P2-bis(2-cyanoethyl) pyrophosphate in the nucleoside triphosphate synthesis. Chemical \u0026 Pharmaceutical Bulletin (1963), 11(11), 1358-63.","chebi_id":"18077","hmdb_id":"HMDB01342","kegg_id":"C00459","pubchem_id":"64968","cs_id":"24604737","foodb_id":null,"wikipedia_link":"Deoxythymidine_triphosphate","biocyc_id":"TTP","iupac":"{[hydroxy({[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})phosphoryl]oxy}phosphonic acid","traditional_iupac":"dTTP","logp":"-2.086216578666666","pka":"2.5314813591657925","alogps_solubility":"9.52e+00 g/l","alogps_logp":"-0.39","alogps_logs":"-1.70","acceptor_count":"11","donor_count":"6","rotatable_bond_count":"8","polar_surface_area":"238.68999999999994","refractivity":"88.03069999999998","polarizability":"36.59837789743729","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"-3.24034425909658","pka_strongest_acidic":"0.8952835615680885","bioavailability":"0","number_of_rings":"2","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2'-Deoxythymidine 5'-triphosphate","2'-Deoxythymidine triphosphate","5-Methyl-dUTP","5'-TTP","Deoxy-TTP","Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dThd5'PPP","dTTP","pppdT","Thymidine 5'-triphosphate","Thymidine 5'-triphosphic acid","Thymidine mono(tetrahydrogen triphosphate)","thymidine triphosphate","THYMIDINE-5'-TRIPHOSPHATE","TTP","ttp, thymidine 5-triphosphate"],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"purine nucleotides de novo biosynthesis","kegg_map_id":null}],"growth_conditions":[{"growth_media":"YEPD medium","concentration":"70.0","concentration_units":"\u0026#181;M","error":"0.0"}],"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":20961955,"citation":"Kumar, D., Abdulovic, A. L., Viberg, J., Nilsson, A. K., Kunkel, T. A., Chabes, A. (2011). \"Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools.\" Nucleic Acids Res 39:1360-1371."},{"pubmed_id":19448611,"citation":"Kim, N., Jinks-Robertson, S. (2009). \"dUTP incorporation into genomic DNA is linked to transcription in yeast.\" Nature 459:1150-1153."},{"pubmed_id":16314323,"citation":"Dornfeld, K., Johnson, M. (2005). \"AP endonuclease deficiency results in extreme sensitivity to thymidine deprivation.\" Nucleic Acids Res 33:6644-6653."},{"pubmed_id":14573610,"citation":"Koc, A., Wheeler, L. J., Mathews, C. K., Merrill, G. F. (2004). \"Hydroxyurea arrests DNA replication by a mechanism that preserves basal dNTP pools.\" J Biol Chem 279:223-230."}],"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":" 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":"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":"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":" purine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" purine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" CTP biosynthetic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleoside triphosphate biosynthetic process"},{"category":"Process","description":" purine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine ribonucleoside triphosphate biosynthetic process"},{"category":"Process","description":" purine nucleotide biosynthetic process"},{"category":"Process","description":" UTP biosynthetic process"},{"category":"Process","description":" GTP 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"}]}