dTTP (YMDB00745)

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Identification

YMDB ID

YMDB00745

Name

dTTP

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

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]

Structure

MOL SDF PDB SMILES InChI

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
2'-Deoxythymidine triphosphoric acid
Deoxythymidine 5'-triphosphoric acid
Deoxythymidine triphosphoric acid
THYMIDINE-5'-triphosphoric acid
Thymidine 5'-triphosphoric acid
Thymidine 5'-triphosphate, magnesium salt
Thymidine 5'-triphosphate, trisodium salt
2'-Deoxythymidine-5'-triphosphate
Thymidine 5'-triphosphate, p''-(32)p-labeled
2’-Deoxythymidine 5’-triphosphate
2’-Deoxythymidine triphosphate
5’-TTP
Deoxythymidine 5’-triphosphate
Thymidine 5’-triphosphate

CAS number

365-08-2

Weight

Average: 482.1683
Monoisotopic: 481.989262798

InChI Key

NHVNXKFIZYSCEB-XLPZGREQSA-N

InChI

InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1

IUPAC Name

{[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 Name

dTTP

Chemical Formula

C₁₀H₁₇N₂O₁₄P₃

SMILES

CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O2)C(=O)NC1=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside triphosphates. These are pyrimidine nucleotides with a triphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine deoxyribonucleotides

Direct Parent

Pyrimidine 2'-deoxyribonucleoside triphosphates

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside triphosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Secondary alcohol
Urea
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-triphosphate (CHEBI:18077 )
thymidine phosphate (CHEBI:18077 )
Deoxyribonucleotides (C00459 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	9.52 g/L	ALOGPS
logP	-0.39	ALOGPS
logP	-2.1	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	0.9	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	238.69 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	88.03 m³·mol⁻¹	ChemAxon
Polarizability	36.6 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Pyrimidine metabolism	PW002469
purine nucleotides de novo biosynthesis	PW002478

KEGG Pathways

Pyrimidine metabolism

ec00240

SMPDB Reactions

Adenosine triphosphate + dTDP → ADP + dTTP

KEGG Reactions

dTDP + Adenosine triphosphate ↔ dTTP + ADP

Concentrations

Intracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
70 ± 0 µM	YEPD medium	aerobic	Baker's yeast	PMID: 14573610
Conversion Details Here

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9742300000-c721ba5109dede8a518b	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00dl-9305110000-bbc51754a929afc4eb54	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-0000900000-d176c8e8a9bdb2d457e5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-0000900000-d176c8e8a9bdb2d457e5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-0900000000-970154df2a1ed9a84a2f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 15V, negative	splash10-001i-0000900000-50c7a1492866ca00359d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, negative	splash10-001i-0200900000-dda4f6996cabd8db242f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 20V, negative	splash10-053r-0602900000-0390bef6ad193f2b5004	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 23V, negative	splash10-0a59-0902600000-2f2a5a489951a9c68992	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 26V, negative	splash10-0a4i-0912200000-1d8c5b170f87fa6f2c9b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 34V, negative	splash10-0a4i-1921100000-93f84465717aa16d3f7c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 41V, negative	splash10-0a4i-2920000000-6d1131e45ff20126cf41	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 50V, negative	splash10-0a6r-5910000000-2a9eb44864392efb37c3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 59V, negative	splash10-056r-9700000000-71a33ac9eaf4e714b558	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 73V, negative	splash10-004i-9200000000-0667d2c3d019b5ca17bc	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 33V, negative	splash10-001i-0209200000-ed0d460f9e1d08011f06	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 33V, negative	splash10-004i-9000000000-5ef060d5ec4b80c35c1a	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 33V, negative	splash10-0a4i-0190000000-e8bf71168cfd7e675dca	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 33V, negative	splash10-001r-0019000000-d84a6f61ca04e6970204	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 16V, negative	splash10-001i-0009000000-6f966eb3b101b9fadfbe	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, negative	splash10-001i-0019000000-f7153b7fadabb2f7f79f	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-9c496d7377af5eb651b2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2901000000-99a48a5d17f022d6494c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-889ecd9966747af96efe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-053i-1410900000-cc4f8db45f53046b5380	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-057r-9870100000-6cf02bd6b66f7b822525	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-cde9ec4f970230e9f180	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

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 26:1155-1160.18846089
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 39:1360-1371.20961955
Kim, N., Jinks-Robertson, S. (2009). "dUTP incorporation into genomic DNA is linked to transcription in yeast." Nature 459:1150-1153.19448611
Dornfeld, K., Johnson, M. (2005). "AP endonuclease deficiency results in extreme sensitivity to thymidine deprivation." Nucleic Acids Res 33:6644-6653.16314323
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 279:223-230.14573610

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 & Pharmaceutical Bulletin (1963), 11(11), 1358-63.

External Links:

Resource	Link
CHEBI ID	18077
HMDB ID	HMDB01342
Pubchem Compound ID	64968
Kegg ID	C00459
ChemSpider ID	24604737
FOODB ID	FDB030841
Wikipedia	Deoxythymidine_triphosphate
BioCyc ID	TTP

Enzymes

Protein Details

1. Nucleoside diphosphate kinase

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
Gene Name:: YNK1
Uniprot ID:: P36010
Molecular weight:: 17166.59961

Reactions

ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.

Structure for #<Compound:0xa76850cc>

Enzymes

Reactions