P. aeruginosa Metabolome Database: Deoxyuridine triphosphate (PAMDB000290)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000290

Identification

Name:

Deoxyuridine triphosphate

Description:

Deoxyuridine triphosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Inosine triphosphate pyrophosphatase, Uridine-cytidine kinase 1, Nucleoside diphosphate kinase 3, Nucleoside diphosphate kinase B, Nucleoside diphosphate kinase 6, Nucleoside diphosphate kinase homolog 5, Nucleoside diphosphate kinase A and Nucleoside diphosphate kinase 7.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

2'-Deoxyuridine 5'-triphosphate
2'-Deoxyuridine 5'-triphosphoric acid
2'-Deoxyuridine-5'-triphosphate
2'-Deoxyuridine-5'-triphosphate = dUTP
2'-Deoxyuridine-5'-triphosphorate
2'-Deoxyuridine-5'-triphosphorate = dUTP
2'-Deoxyuridine-5'-triphosphoric acid
2'-Deoxyuridine-5'-triphosphoric acid = dUTP
Deoxy-UTP
Deoxyuridine triphosphate
Deoxyuridine triphosphoric acid
Deoxyuridine-5'-Triphosphate
Deoxyuridine-5'-triphosphoric acid
Deoxyuridine-triphosphate
Deoxyuridine-triphosphoric acid
DUTP

Chemical Formula:

C₉H₁₅N₂O₁₄P₃

Average Molecular Weight:

468.1417

Monoisotopic Molecular Weight:

467.973612734

InChI Key:

AHCYMLUZIRLXAA-SHYZEUOFSA-N

InChI:

InChI=1S/C9H15N2O14P3/c12-5-3-8(11-2-1-7(13)10-9(11)14)23-6(5)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,20,21)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

CAS number:

1173-82-6

IUPAC Name:

({[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid

Traditional IUPAC Name:

dUTP

SMILES:

O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O

Chemical Taxonomy

Taxonomy Description

This compound 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
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Oxolane
Urea
Secondary alcohol
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-triphosphate (CHEBI:17625 )
deoxyuridine phosphate (CHEBI:17625 )
Deoxyribonucleotides (C00460 )

Physical Properties

State:

Solid

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	8.63 mg/mL	ALOGPS
logP	-0.12	ALOGPS
logP	-2.5	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	83.67 m³·mol^-1	ChemAxon
Polarizability	34.62 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:

Cytoplasm

Reactions:

Pathways:

Metabolic pathways pae01100
Pyrimidine metabolism pae00240

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0900000000-9dfd5f9811270d9aaab8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3911000000-b480c4f463f71544be8f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-2ba3b00121251c9adda0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01b9-3120900000-dedbedae66448a647f3b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-057u-9430100000-0b81cc8084e6bd0f3088	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-056r-9510000000-a72cd2e823cab077b0e1	View in MoNA

References

References:

Ge YF, Huang YF, Zhang GY, Wang XH, Xu JP: Studies on apoptosis of spermatogenic cells in normal fertile men treated with supraphysiological doses of testosterone undecanoate. Asian J Androl. 1999 Sep;1(3):155-8. Pubmed: 11250785
Gilhar A, Ullmann Y, Karry R, Shalaginov R, Assy B, Serafimovich S, Kalish RS: Ageing of human epidermis: the role of apoptosis, Fas and telomerase. Br J Dermatol. 2004 Jan;150(1):56-63. Pubmed: 14746617
Igarashi T, Brown CR, Byrum RA, Nishimura Y, Endo Y, Plishka RJ, Buckler C, Buckler-White A, Miller G, Hirsch VM, Martin MA: Rapid and irreversible CD4+ T-cell depletion induced by the highly pathogenic simian/human immunodeficiency virus SHIV(DH12R) is systemic and synchronous. J Virol. 2002 Jan;76(1):379-91. Pubmed: 11739702
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Lamperti C, Naini AB, Lucchini V, Prelle A, Bresolin N, Moggio M, Sciacco M, Kaufmann P, DiMauro S: Muscle coenzyme Q10 level in statin-related myopathy. Arch Neurol. 2005 Nov;62(11):1709-12. Pubmed: 16286544
Lee AY, Youm YH, Kim NH, Yang H, Choi WI: Keratinocytes in the depigmented epidermis of vitiligo are more vulnerable to trauma (suction) than keratinocytes in the normally pigmented epidermis, resulting in their apoptosis. Br J Dermatol. 2004 Nov;151(5):995-1003. Pubmed: 15541077
Oosterhuis GJ, Mulder AB, Kalsbeek-Batenburg E, Lambalk CB, Schoemaker J, Vermes I: Measuring apoptosis in human spermatozoa: a biological assay for semen quality? Fertil Steril. 2000 Aug;74(2):245-50. Pubmed: 10927039
Russell J, O'Donoghue JA, Finn R, Koziorowski J, Ruan S, Humm JL, Ling CC: Iodination of annexin V for imaging apoptosis. J Nucl Med. 2002 May;43(5):671-7. Pubmed: 11994533
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	17625
HMDB ID	HMDB01191
Pubchem Compound ID	689
Kegg ID	C00460
ChemSpider ID	58580
Wikipedia ID	Not Available
BioCyc ID	DUTP
EcoCyc ID	DUTP
Ligand Expo	DUT

Enzymes

Protein Details

• Deoxyuridine 5'-triphosphate nucleotidohydrolase

General function:: Involved in hydrolase activity
Specific function:: This enzyme is involved in nucleotide metabolism:it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA
Gene Name:: dut
Locus Tag:: PA5321
Molecular weight:: 15.9 kDa

Reactions

dUTP + H(2)O = dUMP + diphosphate.

Protein Details

• 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
Gene Name:: ndk
Locus Tag:: PA3807
Molecular weight:: 15.6 kDa

Reactions

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Protein Details

• Anaerobic ribonucleoside-triphosphate reductase-activating protein

General function:: Involved in [formate-C-acetyltransferase]-activating enzyme activity
Specific function:: Activation of anaerobic ribonucleoside-triphosphate reductase under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine
Gene Name:: nrdG
Locus Tag:: PA1919
Molecular weight:: 25.7 kDa

Protein Details

• Protein mazG

General function:: Involved in nucleoside-triphosphate diphosphatase activity
Specific function:: Specific function unknown
Gene Name:: mazG
Locus Tag:: PA0935
Molecular weight:: 31.2 kDa

Reactions

ATP + H(2)O = AMP + diphosphate.

Protein Details

• Anaerobic ribonucleoside-triphosphate reductase

General function:: Involved in catalytic activity
Specific function:: 2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin
Gene Name:: nrdD
Locus Tag:: PA1920
Molecular weight:: 76.1 kDa

Reactions

2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.

Protein Details

• Nucleoside-triphosphatase rdgB

General function:: Involved in hydrolase activity
Specific function:: Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non- standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions
Gene Name:: rdgB
Locus Tag:: PA0387
Molecular weight:: 21.2 kDa

Reactions

A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate.

Protein Details

• Adenylate kinase

General function:: Involved in ATP binding
Specific function:: Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:: adk
Locus Tag:: PA3686
Molecular weight:: 23.1 kDa

Reactions

ATP + AMP = 2 ADP.

Deoxyuridine triphosphate (PAMDB000290)

Structure for Deoxyuridine triphosphate (PAMDB000290)

Enzymes

Reactions

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