Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:08:16 UTC
HMDB IDHMDB00296
Secondary Accession NumbersNone
Metabolite Identification
Common NameUridine
DescriptionUridine is a molecule (known as a nucleoside) that is formed when uracil is attached to a ribose ring (also known as a ribofuranose) via a b-N1-glycosidic bond. (Wikipedia).
Structure
Thumb
Synonyms
  1. 1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  2. 1-b-D-Ribofuranosyluracil
  3. 1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  4. 1-beta-delta-Ribofuranosyluracil
  5. b-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1
  6. b-Uridine
  7. beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1
  8. beta-Uridine
  9. Uridin
Chemical FormulaC9H12N2O6
Average Molecular Weight244.2014
Monoisotopic Molecular Weight244.069536126
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Nameuridine
CAS Registry Number58-96-8
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChI KeyDRTQHJPVMGBUCF-XVFCMESISA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleosides and Analogues
Sub ClassN/A
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • a pyrimidine ribonucleoside(Cyc)
Substituents
  • 1,2 Diol
  • Glycosyl Compound
  • Hydropyrimidine
  • N Glycosyl Compound
  • Oxolane
  • Pentose Monosaccharide
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Saccharide
  • Secondary Alcohol
Direct ParentPyrimidine Nucleosides and Analogues
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point163 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.98HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
water solubility135 g/LALOGPS
logP-1.8ALOGPS
logP-2.4ChemAxon
logS-0.26ALOGPS
pKa (strongest acidic)9.7ChemAxon
pKa (strongest basic)-3ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count6ChemAxon
hydrogen donor count4ChemAxon
polar surface area119.33ChemAxon
rotatable bond count2ChemAxon
refractivity52.57ChemAxon
polarizability21.78ChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified3.10 (2.90-3.30) uMAdult (>18 years old)BothNormal
BloodDetected and Quantified3.12 +/- 1.31 uMAdult (>18 years old)BothNormal
UrineDetected and Quantified0.22 +/- 0.07 umol/mmol creatinineAdult (>18 years old)MaleNormal
UrineDetected and Quantified0.21 +/- 0.08 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified0.21 +/- 0.09 umol/mmol creatinineAdult (>18 years old)FemaleNormal
UrineDetected and Quantified0.994 (0.637-1.351) umol/mmol creatinineAdult (>18 years old)BothNormal
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified7.7 +/- 0.9 uMAdult (>18 years old)BothLesch-Nyhan syndrome
BloodDetected and Quantified4.23 +/- 1.92 uMAdult (>18 years old)BothCanavan disease
Cerebrospinal Fluid (CSF)Detected and Quantified2.30 (1.90-2.70) uMAdult (>18 years old)BothDegenerative disc disease
Associated Disorders and Diseases
Disease References
Canavan disease
  • Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832
Degenerative disc disease
  • Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. Pubmed: 6656991
Lesch-Nyhan syndrome
  • Harkness RA, McCreanor GM, Watts RW: Lesch-Nyhan syndrome and its pathogenesis: purine concentrations in plasma and urine with metabolite profiles in CSF. J Inherit Metab Dis. 1988;11(3):239-52. Pubmed: 3148065
Associated OMIM IDs
DrugBank IDDB02745
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB007411
KNApSAcK IDC00019674
Chemspider ID5807
KEGG Compound IDC00299
BioCyc IDURIDINE
BiGG ID34541
Wikipedia LinkUridine
NuGOwiki LinkHMDB00296
Metagene LinkHMDB00296
METLIN ID90
PubChem Compound6029
PDB IDURI
ChEBI ID16704
References
Synthesis ReferenceDoi, Muneharu; Asahi, Satoru; Izawa, Motoo. Fermentative production of uridine and cytidine. Baiosaiensu to Indasutori (1993), 51(12), 972-6.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. Pubmed: 6656991
  2. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. Pubmed: 15116424

Enzymes

Gene Name:
NT5E
Uniprot ID:
P21589
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Reactions
Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine unknown dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine unknown dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphatedetails
Gene Name:
UCK2
Uniprot ID:
Q9BZX2
Reactions
Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine unknown dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine unknown dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphatedetails
10. AID
Gene Name:
AID
Uniprot ID:
Q546Y9
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
NT5C2
Uniprot ID:
P49902
Reactions
Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric aciddetails
Gene Name:
CDA
Uniprot ID:
P32320
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
UPP1
Uniprot ID:
Q16831
Reactions
Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphatedetails
Gene Name:
UPP2
Uniprot ID:
O95045
Reactions
Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphatedetails
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Reactions
Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine unknown dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine unknown dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphatedetails
Gene Name:
PUS3
Uniprot ID:
Q9BZE2
Gene Name:
PUSL1
Uniprot ID:
Q8N0Z8
Gene Name:
APOBEC3H
Uniprot ID:
Q6NTF7
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3A
Uniprot ID:
P31941
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3B
Uniprot ID:
Q9UH17
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3C
Uniprot ID:
Q9NRW3
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3D
Uniprot ID:
Q96AK3
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
APOBEC3F
Uniprot ID:
Q8IUX4
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails
Gene Name:
AICDA
Uniprot ID:
Q9GZX7
Reactions
Cytidine + Water unknown Uridine + Ammoniadetails