Record Information
Version2.0
Creation Date2012-05-31 13:03:12 -0600
Update Date2015-09-17 15:41:07 -0600
Secondary Accession Numbers
  • ECMDB01000
Identification
Name:dUDP
Description:dUDP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleoside Diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. Deoxyuridine Diphosphate (dUDP) dUDP is a deoxyribonucleotide made from UDP in the reaction catalyzed by ribonucleotide reductase, as follows: UDP + NADPH <=> dUDP + NADP+ (http://www.pearsonhighered.com/mathews/molex/dudp.htm)
Structure
Thumb
Synonyms:
  • 2'-Deoxyuridine-5'-diphosphate
  • 2'-Deoxyuridine-5'-diphosphoric acid
  • Deoxyuridine-diphosphate
  • Deoxyuridine-diphosphoric acid
  • DUDP
Chemical Formula:C9H14N2O11P2
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
CAS number:Not Available
IUPAC Name:[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name:deoxyuridine-5'-diphosphate
SMILES:O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
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 DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility8.03 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity72.8 m3·mol-1ChemAxon
Polarizability30.47 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
KEGG Pathways:
EcoCyc Pathways:
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-8f7f3f11f218527956e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-4910000000-25f5ee65cf43240b006fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6900000000-95e461eef231ae093595View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000l-3309000000-52c15d9412bfdd9580b7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9601000000-9a1ca925d25e95e30f48View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-06486339ea40829dd0bcView in MoNA
References
References:
  • 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
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDHMDB01000
Pubchem Compound ID687
Kegg IDC01346
ChemSpider ID667
Wikipedia IDNot Available
BioCyc IDDUDP
EcoCyc IDDUDP

Enzymes

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. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
Gene Name:
nrdA
Uniprot ID:
P00452
Molecular weight:
85774
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth
Gene Name:
tmk
Uniprot ID:
P0A720
Molecular weight:
23783
Reactions
ATP + dTMP = ADP + dTDP.
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
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
udk
Uniprot ID:
P0A8F4
Molecular weight:
24353
Reactions
ATP + uridine = ADP + UMP.
ATP + cytidine = ADP + CMP.
General function:
Involved in electron carrier activity
Specific function:
Efficient electron donor for the essential enzyme ribonucleotide reductase. Is also able to reduce the interchain disulfide bridges of insulin
Gene Name:
trxC
Uniprot ID:
P0AGG4
Molecular weight:
15555
Reactions
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H.
General function:
Involved in catalytic activity
Specific function:
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin
Gene Name:
nrdD
Uniprot ID:
P28903
Molecular weight:
80022
Reactions
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F contains the tyrosyl radical required for catalysis
Gene Name:
nrdF
Uniprot ID:
P37146
Molecular weight:
36443
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide
Gene Name:
nrdE
Uniprot ID:
P39452
Molecular weight:
80478
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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
Uniprot ID:
P69441
Molecular weight:
23586
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Gene Name:
nrdB
Uniprot ID:
P69924
Molecular weight:
43517
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Uniprot ID:
P0AC69
Molecular weight:
12879
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxC
Uniprot ID:
P0AC62
Molecular weight:
9137
General function:
Involved in protein binding
Specific function:
Involved in reducing some disulfides in a coupled system with glutathione reductase. Does not act as hydrogen donor for ribonucleotide reductase
Gene Name:
grxB
Uniprot ID:
P0AC59
Molecular weight:
24350
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxA
Uniprot ID:
P68688
Molecular weight:
9685
General function:
Involved in electron carrier activity
Specific function:
Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
Gene Name:
trxA
Uniprot ID:
P0AA25
Molecular weight:
11807

Transporters

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
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.