Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000123
Identification
Name: Uridine 5'-diphosphate
Description:Uridine 5'-diphosphate, also known as UDP, is an uracil nucleotide containing a pyrophosphate group esterified to C5 of the sugar moiety. UDP is an important extracellular pyrimidine signaling molecule that mediates diverse biological effects via P1 and P2 purinergic receptors, such as the uptake of thymidine and proliferation of gliomas. UDP induces intracellular Ca(2+) responses and oscillations in HeLa cells, due to the activation of P2Ys (G-protein coupled ATP receptors).
Structure
Thumb
Synonyms:
  • 5'-UDP
  • UDP
  • Uridine 5'-diphosphate
  • Uridine 5'-diphosphoric acid
  • Uridine 5'-pyrophosphate
  • Uridine 5'-pyrophosphorate
  • Uridine 5'-pyrophosphoric acid
  • Uridine diphosphate
  • Uridine diphosphoric acid
  • Uridine pyrophosphate
  • Uridine pyrophosphoric acid
  • Uridine-5'-diphosphate
  • Uridine-5'-diphosphoric acid
  • Uridine-diphosphate
  • Uridine-diphosphoric acid
Chemical Formula: C9H14N2O12P2
Average Molecular Weight: 404.1612
Monoisotopic Molecular Weight: 404.002196946
InChI Key: XCCTYIAWTASOJW-XVFCMESISA-N
InChI:InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
CAS number: 58-98-0
IUPAC Name:[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name: UDP
SMILES:O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility8.89 mg/mLALOGPS
logP-0.94ALOGPS
logP-3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area212.39 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.31 m3·mol-1ChemAxon
Polarizability30.41 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Reduced Thioredoxin + Uridine 5'-diphosphate > dUDP + Water + Oxidized Thioredoxin
glutaredoxin + Uridine 5'-diphosphate > dUDP + glutaredoxin + Water
Adenosine triphosphate + Uridine 5'-diphosphate <> ADP + Uridine triphosphate
Adenosine triphosphate + Uridine 5'-monophosphate <> ADP + Uridine 5'-diphosphate
Uridine diphosphate-N-acetylglucosamine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > Hydrogen ion + Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate
2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + UDP-2,3-Bis(3-hydroxytetradecanoyl)glucosamine <> Hydrogen ion + 2,3,2',3'-Tetrakis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1-phosphate + Uridine 5'-diphosphate
Glucose 6-phosphate + UDP-Glucose > Hydrogen ion + Trehalose 6-phosphate + Uridine 5'-diphosphate
O-Acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate + UDP-Glucose > Glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate + Hydrogen ion + Uridine 5'-diphosphate
Glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate + UDP-D-Galacto-1,4-furanose > Galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate + Hydrogen ion + Uridine 5'-diphosphate
Undecaprenyl phosphate + Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose > Undecaprenyl phosphate-4-amino-4-formyl-L-arabinose + Uridine 5'-diphosphate
glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A + UDP-Glucose > glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A + Hydrogen ion + Uridine 5'-diphosphate
galactosyl-glucosyl-inner core oligosaccharide lipid A + UDP-Glucose > glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A + Hydrogen ion + Uridine 5'-diphosphate
glucosyl-inner core oligosaccharide lipid A + UDP-Glucose > galactosyl-glucosyl-inner core oligosaccharide lipid A + Hydrogen ion + Uridine 5'-diphosphate
inner core oligosaccharide lipid A (E coli) + UDP-Glucose > glucosyl-inner core oligosaccharide lipid A + Hydrogen ion + Uridine 5'-diphosphate
UDP-N-Acetyl-D-mannosaminouronate + Undecaprenyl-N-acetyl-alpha-D-glucosaminyl-pyrophosphate > Hydrogen ion + Uridine 5'-diphosphate + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate
Uridine diphosphate-N-acetylglucosamine + Water <> N-Acetylmannosamine + Uridine 5'-diphosphate
RNA + Phosphate <> RNA + Uridine 5'-diphosphate
Uridine triphosphate + Cytidine <> Uridine 5'-diphosphate + Cytidine monophosphate
Uridine triphosphate + Uridine <> Uridine 5'-diphosphate + Uridine 5'-monophosphate
UDP-Glucose + LPS (1-O-antigen) <> Uridine 5'-diphosphate + D-Glucosyllipopolysaccharide
dUDP + Thioredoxin disulfide + Water <> Thioredoxin + Uridine 5'-diphosphate
UDP-Glucose + Glucose 6-phosphate <> Uridine 5'-diphosphate + Trehalose 6-phosphate
UDP-Glucose + Cellulose <> Uridine 5'-diphosphate + Cellulose
Uridine triphosphate + D-Tagatose 6-phosphate <> Uridine 5'-diphosphate + D-Tagatose 1,6-bisphosphate
UDP-2,3-Bis(3-hydroxytetradecanoyl)glucosamine + 2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate <> Uridine 5'-diphosphate + 2,3,2',3'-Tetrakis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1-phosphate
Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine diphosphate-N-acetylglucosamine <> Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate
MurAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala)-diphospho-undecaprenol + Uridine diphosphate-N-acetylglucosamine <> Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine + Uridine 5'-diphosphate
Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose + Di-trans,poly-cis-undecaprenyl phosphate <> Undecaprenyl phosphate alpha-L-Ara4FN + Uridine 5'-diphosphate + 4-Amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate
Uridine diphosphate-N-acetylglucosamine poly-&beta;-1,6-N-acetyl-D-glucosamine + Uridine 5'-diphosphate
a lipopolysaccharide + Uridine diphosphate-N-acetylglucosamine a <i>N</i>-acetyl-D-glucosaminyl-lipopolysaccharide + Uridine 5'-diphosphate
UDP-Glucose + a lipopolysaccharide D-glucosyl-lipopolysaccharide + Uridine 5'-diphosphate
N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol + Uridine diphosphate-N-acetylglucosamine <> Hydrogen ion + N-Acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine + Uridine 5'-diphosphate
Uridine 5'-diphosphate + Water > Phosphate + Uridine 5'-monophosphate + Hydrogen ion
Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose + Di-trans,poly-cis-undecaprenyl phosphate > 4-deoxy-4-formamido-&alpha;-L-arabinopyranosyl <i>ditrans,octacis</i>-undecaprenyl phosphate + Uridine 5'-diphosphate
UDP-Glucose + Heptosyl2-KDO2-lipid A > Hydrogen ion + Glucosyl-heptosyl2-KDO2-lipid A + Uridine 5'-diphosphate
Glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + Uridine diphosphategalactose > Hydrogen ion + Galactosyl-glucosyl-heptosyl3-KDO2-lipid A-bisphosphate + Uridine 5'-diphosphate
UDP-Glucose + Galactosyl-glucosyl-heptosyl3-KDO2-lipid A-bisphosphate > Hydrogen ion + Galactosyl-glucosyl2-heptosyl3-KDO2-lipid A-bisphosphate + Uridine 5'-diphosphate
UDP-Glucose + Galactosyl-glucosyl2-heptosyl3-KDO2-lipid A-bisphosphate > Hydrogen ion + Galactosyl-glucosyl3-heptosyl3-KDO2-lipid A-bisphosphate + Uridine 5'-diphosphate
UDP-Glucose + &alpha;-D-glucose 6-phosphate > Hydrogen ion + Uridine 5'-diphosphate + Trehalose 6-phosphate
Undecaprenyl-N-acetyl-alpha-D-glucosaminyl-pyrophosphate + UDP-N-Acetyl-D-mannosaminouronate <> Hydrogen ion + Undecaprenyl phosphate + Uridine 5'-diphosphate
UDP-Glucose + (1,4-beta-D-glucosyl)(n) > Uridine 5'-diphosphate + (1,4-beta-D-glucosyl)(n+1)
UDP-2,3-Bis(3-hydroxytetradecanoyl)glucosamine + 2,3-bis((3R)-3-hydroxymyristoyl)-beta-D-glucosaminyl 1-phosphate > Uridine 5'-diphosphate + 2,3-bis(3-Hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate
Uridine diphosphate-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol > Uridine 5'-diphosphate + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
Uridine diphosphategalactose + LPS (1-O-antigen) > Uridine 5'-diphosphate + 3-alpha-D-galactosyl-[lipopolysaccharide glucose]
UDP-Glucose + LPS (1-O-antigen) > Uridine 5'-diphosphate + D-glucosyl-lipopolysaccharide
Uridine diphosphate-N-acetylglucosamine + LPS (1-O-antigen) > Uridine 5'-diphosphate + N-acetyl-D-glucosaminyllipopolysaccharide
Uridine diphosphate-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol <> Uridine 5'-diphosphate + Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine
Adenosine triphosphate + dCMP + Uridine 5'-monophosphate <> ADP + dCDP + Uridine 5'-diphosphate
N-Acetyl-D-glucosaminyldiphospho-di-trans,octa-cis-undecaprenol <> Uridine 5'-diphosphate
UDP-Glucose <> Uridine 5'-diphosphate
Uridine diphosphate-N-acetylglucosamine + LPS (1-O-antigen) <> Uridine 5'-diphosphate
2,3-bis[(3R)-3-hydroxymyristoyl]-α-D-glucosaminyl 1-phosphate + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine > Uridine 5'-diphosphate + Hydrogen ion + (2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl)-(1->6)-(2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl phosphate)
(heptosyl)2-Kdo2-lipid A + UDP-Glucose > Uridine 5'-diphosphate + Hydrogen ion + glucosyl-(heptosyl)2-Kdo2-lipid A
glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP-α-D-galactose > galactosyl-glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate + Uridine 5'-diphosphate + Hydrogen ion
galactosyl-glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP-Glucose > Uridine 5'-diphosphate + Hydrogen ion + galactosyl-(glucosyl)2-(heptosyl)3-Kdo2-lipid A-bisphosphate
galactosyl-(glucosyl)2-(heptosyl)3-Kdo2-lipid A-bisphosphate + UDP-Glucose > Uridine 5'-diphosphate + Hydrogen ion + galactosyl-(glucosyl)3-(heptosyl)3-Kdo2-lipid A-bisphosphate
UDP-4-Deoxy-4-formamido-beta-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate > Uridine 5'-diphosphate + 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate
Uridine 5'-diphosphate + Adenosine triphosphate + Uridine 5'-diphosphate > Uridine triphosphate + Adenosine diphosphate + Uridine triphosphate + ADP
Uridine 5'-diphosphate + reduced thioredoxin + Uridine 5'-diphosphate oxidized thioredoxin + Water + dUDP + dUDP
Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine diphosphate-N-acetylglucosamine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > Uridine 5'-diphosphate + Hydrogen ion + lipid II(A) + Uridine 5'-diphosphate
UDP-Glucose + Alpha-D-glucose 6-phosphate > Uridine 5'-diphosphate + Trehalose 6-phosphate + Hydrogen ion + Uridine 5'-diphosphate
Uridine 5'-monophosphate + Adenosine triphosphate > Adenosine diphosphate + Uridine 5'-diphosphate + ADP + Uridine 5'-diphosphate
N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol + UDP-ManNAcA > Uridine 5'-diphosphate + Hydrogen ion + Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate pyrophosphate + Uridine 5'-diphosphate + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-73234233232c376d095cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0002-9000000000-7c065a8df0e08b8c365fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0pdi-6910600000-bf4136774851b6559f17View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
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  • 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
  • Morrone, F. B., Jacques-Silva, M. C., Horn, A. P., Bernardi, A., Schwartsmann, G., Rodnight, R., Lenz, G. (2003). "Extracellular nucleotides and nucleosides induce proliferation and increase nucleoside transport in human glioma cell lines." J Neurooncol 64:211-218. Pubmed: 14558596
  • Rise, A. (1976). "[Drugs and the fetus]." Tidsskr Nor Laegeforen 96:41-42. Pubmed: 1257952
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  • Syme MR, Paxton JW, Keelan JA: Drug transfer and metabolism by the human placenta. Clin Pharmacokinet. 2004;43(8):487-514. Pubmed: 15170365
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  • 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: Zeng, Bin; Rao, Linfan; Li, Gaowo. Method for manufacturing uridine diphosphate. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 14pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17659
HMDB IDHMDB00295
Pubchem Compound ID6031
Kegg IDC00015
ChemSpider ID5809
WikipediaUDP
BioCyc IDUDP
EcoCyc IDUDP
Ligand ExpoUDP