dUDP (YMDB00746)

Identification

YMDB ID

YMDB00746

Name

dUDP

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

dUDP belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dUDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dUDP exists in all eukaryotes, ranging from yeast to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

2-deoxyuridine 5-diphosphate
2'-Deoxyuridine 5'-diphosphate
2'-deoxyuridine-5'-diphosphate
deoxyuridine-diphosphate
dUDP
2'-Deoxyuridine 5'-diphosphoric acid
2'-Deoxyuridine 5'-(trihydrogen diphosphate)
2’-Deoxyuridine 5’-(trihydrogen diphosphate)
2’-Deoxyuridine 5’-diphosphate
Deoxyuridine 5'-diphosphate
Deoxyuridine 5’-diphosphate
Deoxyuridine diphosphate

CAS number

4208-67-7

Weight

Average: 388.1618
Monoisotopic: 388.007282324

InChI Key

QHWZTVCCBMIIKE-SHYZEUOFSA-N

InChI

InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

IUPAC Name

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

Traditional IUPAC Name

dUDP

Chemical Formula

C₉H₁₄N₂O₁₁P₂

SMILES

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

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate 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 diphosphates

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:28850 )
deoxyuridine phosphate (CHEBI:28850 )
Deoxyribonucleotides (C01346 )

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	8.03 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-2.1	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	192.16 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.8 m³·mol⁻¹	ChemAxon
Polarizability	29.83 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

nucleus
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Pyrimidine metabolism

PW002469

KEGG Pathways

Pyrimidine metabolism

ec00240

SMPDB Reactions

dUDP + Adenosine triphosphate → ADP + Deoxyuridine triphosphate

Uridine 5'-diphosphate + reduced thioredoxin oxidized thioredoxin + water + dUDP

Uridine 5'-diphosphate + a reduced NrdH glutaredoxin-like protein → water + an oxidized NrdH glutaredoxin-like protein + dUDP

KEGG Reactions

Adenosine triphosphate + dUDP ↔ Deoxyuridine triphosphate + ADP

thioredoxin dithiol + Uridine 5'-diphosphate → thioredoxin disulfide + water + dUDP

Adenosine triphosphate + dUMP ↔ dUDP + ADP

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004m-6911000000-1f7795debc1eaf0802e6	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-002g-9741200000-2a5ff084260317ace541	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-3d46a12380fc537ed482	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4910000000-e4d9c69da2a4f1af3f7d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-6900000000-38fc58820b65e6b77481	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-6309000000-e32a735e5de73376968b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056u-9801000000-189cbc835aaa1c3340b1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-07b08a59c26df7bb2d1e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0009000000-aa2d362ee8b723b7d488	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9111000000-b30fec320d4d01519c03	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-5632c2fa3d2d7c954d90	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-3913000000-cbd6b90181ad2dcbef10	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-6910000000-514b52784d71478993f8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-4900000000-32241af48bd1f1fd6e37	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

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
Gadsden, M. H., McIntosh, E. M., Game, J. C., Wilson, P. J., Haynes, R. H. (1993). "dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae." EMBO J 12:4425-4431.8223452

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	28850
HMDB ID	HMDB01000
Pubchem Compound ID	687
Kegg ID	C01346
ChemSpider ID	24785517
FOODB ID	FDB022361
Wikipedia ID	Not Available
BioCyc ID	DUDP

Enzymes

Protein Details

1. Uridylate kinase

General function:: Involved in ATP binding
Specific function:: Furnishes the cell with pyrimidines. Accepts UMP, and dUMP as phosphate acceptors with high activity; to a lesser extent, it can also use IMP, GMP, dGMP, 5-iodo-dUMP, XMP, and dTMP as substrates. ATP and dATP are the best phosphate donors; can use GTP, dGTP, dCTP, and dTTP to some degree (30-50%)
Gene Name:: URA6
Uniprot ID:: P15700
Molecular weight:: 22933.0

Reactions

ATP + UMP → ADP + UDP.

Protein Details

2. Ribonucleoside-diphosphate reductase small chain 1

General function:: Involved in oxidoreductase activity
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:: RNR2
Uniprot ID:: P09938
Molecular weight:: 46147.0

Reactions

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.

Protein Details

3. 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.

Protein Details

4. Ribonucleoside-diphosphate reductase large chain 1

General function:: Involved in oxidation-reduction process
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:: RNR1
Uniprot ID:: P21524
Molecular weight:: 99560.20313

Reactions

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.

Protein Details

5. Ribonucleoside-diphosphate reductase small chain 2

General function:: Involved in oxidoreductase activity
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits
Gene Name:: RNR4
Uniprot ID:: P49723
Molecular weight:: 40054.19922

Reactions

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.

Structure for #<Compound:0xa937d2d8>

Enzymes

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