Record Information
Version2.0
Creation Date2012-05-31 10:25:53 -0600
Update Date2015-09-13 12:56:07 -0600
Secondary Accession Numbers
  • ECMDB00295
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. (PMID: 14558596) UDP induces intracellular Ca(2+) responses and oscillations in HeLa cells, due to the activation of P2Ys (G-protein coupled ATP receptors). (PMID: 1257952)
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
Weight:Average: 404.1612
Monoisotopic: 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
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Hydroxypyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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
Adenosine triphosphate + Uridine 5'-diphosphate <> ADP + Uridine triphosphate
Adenosine triphosphate + Uridine 5'-monophosphate <> ADP + Uridine 5'-diphosphate
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
Adenosine triphosphate + Uridine 5'-monophosphate <> ADP + 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
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
octyl alpha-D-glucopyranoside + UDP-D-Galacto-1,4-furanose Hydrogen ion + octyl beta-1,6-D-galactofuranosyl-alpha-D-glucopyranoside + Uridine 5'-diphosphate
UDP-Glucose + &alpha;-D-glucose 6-phosphate > Hydrogen ion + Uridine 5'-diphosphate + Trehalose 6-phosphate
Uridine 5'-diphosphate + Adenosine triphosphate > Uridine triphosphate + ADP
Undecaprenyl-N-acetyl-alpha-D-glucosaminyl-pyrophosphate + UDP-N-Acetyl-D-mannosaminouronate <> Hydrogen ion + Undecaprenyl phosphate + Uridine 5'-diphosphate
UDP-4-Deoxy-4-formamido-beta-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate > Uridine 5'-diphosphate + 4-deoxy-4-formamido-alpha-L-arabinose di-trans,octa-cis-undecaprenyl phosphate
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
UDP-Glucose + Glucose 6-phosphate > Uridine 5'-diphosphate + Trehalose 6-phosphate
Adenosine triphosphate + Uridine 5'-monophosphate > ADP + Uridine 5'-diphosphate
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
UDP-ManNAcA + Und-PP-GlcNAc > Uridine 5'-diphosphate + Und-PP-GlcNAc-ManNAcA
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 + Glucose 6-phosphate <> Uridine 5'-diphosphate + Trehalose 6-phosphate
UDP-Glucose <> Uridine 5'-diphosphate
Uridine diphosphate-N-acetylglucosamine + LPS (1-O-antigen) <> Uridine 5'-diphosphate
Uridine diphosphategalactose + LPS (1-O-antigen) <> Uridine 5'-diphosphate + 3-alpha-D-Galactosyl-[lipopolysaccharide glucose]
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
N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol + Uridine diphosphate-N-acetylglucosamine > Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate + Hydrogen ion
Undecaprenyl-N-acetyl-alpha-D-glucosaminyl-pyrophosphate + UDP-ManNAcA > Uridine 5'-diphosphate + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate + Hydrogen ion
UDP-Glucose + Mannose 6-phosphate > alpha,alpha-Trehalose 6-phosphate + Uridine 5'-diphosphate + Hydrogen ion
More...

SMPDB Pathways:
Amino sugar and nucleotide sugar metabolism IIIPW000895 Pw000895Pw000895 greyscalePw000895 simple
Lipopolysaccharide biosynthesisPW000831 Pw000831Pw000831 greyscalePw000831 simple
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
Secondary Metabolites: enterobacterial common antigen biosynthesisPW000959 Pw000959Pw000959 greyscalePw000959 simple
Secondary Metabolites: enterobacterial common antigen biosynthesis 2PW002045 Pw002045Pw002045 greyscalePw002045 simple
Secondary Metabolites: enterobacterial common antigen biosynthesis 3PW002046 Pw002046Pw002046 greyscalePw002046 simple
Starch and sucrose metabolismPW000941 Pw000941Pw000941 greyscalePw000941 simple
lipopolysaccharide biosynthesis IIPW001905 Pw001905Pw001905 greyscalePw001905 simple
lipopolysaccharide biosynthesis IIIPW002059 Pw002059Pw002059 greyscalePw002059 simple
peptidoglycan biosynthesis IPW000906 Pw000906Pw000906 greyscalePw000906 simple
peptidoglycan biosynthesis I 2PW002062 Pw002062Pw002062 greyscalePw002062 simple
polymyxin resistancePW002052 Pw002052Pw002052 greyscalePw002052 simple
trehalose biosynthesis IPW002088 Pw002088Pw002088 greyscalePw002088 simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
1790± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
386± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
Find out more about how we convert literature concentrations.
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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  • 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
  • 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
  • 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
  • Syme MR, Paxton JW, Keelan JA: Drug transfer and metabolism by the human placenta. Clin Pharmacokinet. 2004;43(8):487-514. Pubmed: 15170365
  • 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: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

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 RNA binding
Specific function:
Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction
Gene Name:
pnp
Uniprot ID:
P05055
Molecular weight:
77100
Reactions
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
Gene Name:
pfkB
Uniprot ID:
P06999
Molecular weight:
32456
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate.
General function:
Involved in cytidylate kinase activity
Specific function:
ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors
Gene Name:
cmk
Uniprot ID:
P0A6I0
Molecular weight:
24746
Reactions
ATP + (d)CMP = ADP + (d)CDP.
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 + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
Gene Name:
pfkA
Uniprot ID:
P0A796
Molecular weight:
34842
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate.
General function:
Involved in cellular amino acid biosynthetic process
Specific function:
Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor
Gene Name:
pyrH
Uniprot ID:
P0A7E9
Molecular weight:
25970
Reactions
ATP + UMP = ADP + UDP.
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 lipid-A-disaccharide synthase activity
Specific function:
Condensation of UDP-2,3-diacylglucosamine and 2,3- diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Gene Name:
lpxB
Uniprot ID:
P10441
Molecular weight:
42382
Reactions
UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate = UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate.
General function:
Involved in undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity
Specific function:
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Gene Name:
murG
Uniprot ID:
P17443
Molecular weight:
37815
Reactions
UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
UDP-glucose + lipopolysaccharide = UDP + D- glucosyl-lipopolysaccharide
Gene Name:
rfaJ
Uniprot ID:
P27129
Molecular weight:
39040
Reactions
UDP-glucose + lipopolysaccharide = UDP + D-glucosyl-lipopolysaccharide.
General function:
Involved in UDP-N-acetylglucosamine 2-epimerase activity
Specific function:
Catalyzes the reversible epimerization at C-2 of UDP-N- acetylglucosamine (UDP-GlcNAc) and thereby provides bacteria with UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues. Also involved in bacteriophage N4 adsorption
Gene Name:
wecB
Uniprot ID:
P27828
Molecular weight:
42244
Reactions
UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-mannosamine.
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 catalytic activity
Specific function:
Catalyzes the transfer of glucose from UDP-glucose to glucose-6-phosphate to form alpha,alpha-1,1 trehalose-6-phosphate. Acts with retention of the anomeric configuration of the UDP-sugar donor. Essential for viability of the cells at low temperatures and at elevated osmotic strength
Gene Name:
otsA
Uniprot ID:
P31677
Molecular weight:
53611
Reactions
UDP-glucose + D-glucose 6-phosphate = UDP + alpha,alpha-trehalose 6-phosphate.
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 cellulose synthase activity
Specific function:
Catalytic subunit of cellulose synthase. It polymerizes uridine 5'-diphosphate glucose to cellulose, which is produced as an extracellular component for mechanical and chemical protection at the onset of the stationary phase, when the cells exhibit multicellular behavior (rdar morphotype). Coexpression of cellulose and thin aggregative fimbriae leads to a hydrophobic network with tightly packed cells embedded in a highly inert matrix
Gene Name:
bcsA
Uniprot ID:
P37653
Molecular weight:
99784
Reactions
UDP-glucose + (1,4-beta-D-glucosyl)(n) = UDP + (1,4-beta-D-glucosyl)(n+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. 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 phosphotransferase activity, for other substituted phosphate groups
Specific function:
Catalyzes the transfer of 4-deoxy-4-formamido-L- arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnC
Uniprot ID:
P77757
Molecular weight:
36339
Reactions
UDP-4-deoxy-4-formamido-beta-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-alpha-L-arabinose di-trans,octa-cis-undecaprenyl phosphate.
General function:
Involved in biosynthetic process
Specific function:
Involved in the addition of the first glucose residue to the lipopolysaccharide core
Gene Name:
rfaG
Uniprot ID:
P25740
Molecular weight:
42284
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
Adds the terminal N-acetyl-D-glucosamine group on the glucose(II) group of LPS
Gene Name:
waaU
Uniprot ID:
P27242
Molecular weight:
41729
Reactions
UDP-N-acetyl-D-glucosamine + lipopolysaccharide = UDP + N-acetyl-D-glucosaminyllipopolysaccharide.
General function:
Involved in biosynthetic process
Specific function:
Adds a galactose goup to a glucose group of LPS
Gene Name:
rfaB
Uniprot ID:
P27127
Molecular weight:
40826
General function:
Involved in biosynthetic process
Specific function:
May be a glycosyltransferase involved in the transfer of UDP-GalF and UDP-glucose
Gene Name:
yefI
Uniprot ID:
P37751
Molecular weight:
43188
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 transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the synthesis of Und-PP-GlcNAc-ManNAcA (Lipid II), the second lipid-linked intermediate involved in ECA synthesis
Gene Name:
wecG
Uniprot ID:
P27836
Molecular weight:
27928
Reactions
UDP-ManNAcA + Und-PP-GlcNAc = UDP + Und-PP-GlcNAc-ManNAcA.
General function:
Involved in lipopolysaccharide-1,6-galactosyltransferas
Specific function:
May be a glycosyltransferase involved in the transfer of UDP-GalF to the lipopolysaccharide
Gene Name:
yefG
Uniprot ID:
P37749
Molecular weight:
37757
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
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
UDP-galactose + lipopolysaccharide = UDP + 3- alpha-D-galactosyl-[lipopolysaccharide glucose]
Gene Name:
rfaI
Uniprot ID:
P27128
Molecular weight:
39423
Reactions
UDP-galactose + lipopolysaccharide = UDP + 3-alpha-D-galactosyl-[lipopolysaccharide glucose].

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.