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dUDP (YMDB00746)

Identification
YMDB IDYMDB00746
NamedUDP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondUDP 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. Within yeast, dUDP participates in a number of enzymatic reactions. In particular, dUDP can be biosynthesized from uridine 5'-diphosphate; which is mediated by the enzyme ribonucleoside diphosphate reductase 1. In addition, dUDP can be converted into deoxyuridine triphosphate; which is mediated by the enzyme nucleoside diphosphate kinase. In yeast, dUDP is involved in the metabolic pathway called the pyrimidine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-deoxyuridine 5-diphosphate
  • 2'-Deoxyuridine 5'-diphosphate
  • 2'-deoxyuridine-5'-diphosphate
  • deoxyuridine-diphosphate
  • dUDP
  • 2'-Deoxyuridine 5'-diphosphoric acid
CAS number4208-67-7
WeightAverage: 388.1618
Monoisotopic: 388.007282324
InChI KeyQHWZTVCCBMIIKE-SHYZEUOFSA-N
InChIInChI=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 NamedUDP
Chemical FormulaC9H14N2O11P2
SMILESO[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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility8.03 g/LALOGPS
logP-0.99ALOGPS
logP-2.1ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity72.8 m³·mol⁻¹ChemAxon
Polarizability29.83 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
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 ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004m-6911000000-1f7795debc1eaf0802e6JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-002g-9741200000-2a5ff084260317ace541JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-3d46a12380fc537ed482JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4910000000-e4d9c69da2a4f1af3f7dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-38fc58820b65e6b77481JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-6309000000-e32a735e5de73376968bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056u-9801000000-189cbc835aaa1c3340b1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-07b08a59c26df7bb2d1eJSpectraViewer
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:
ResourceLink
CHEBI ID28850
HMDB IDHMDB01000
Pubchem Compound ID687
Kegg IDC01346
ChemSpider ID24785517
FOODB IDFDB022361
Wikipedia IDNot Available
BioCyc IDDUDP

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.