You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
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 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 Solubility135.0ALOGPS
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 Area119.33 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.57 m3·mol-1ChemAxon
Polarizability21.78 Å3ChemAxon
Spectra
SpectraGC-MSMS/MSLC-MS1D NMR2D NMR
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
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified3.10 (2.90-3.30) uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified3.12 +/- 1.31 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.22 +/- 0.07 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified0.21 +/- 0.08 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.21 +/- 0.09 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified0.994 (0.637-1.351) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified7.7 +/- 0.9 uMAdult (>18 years old)BothLesch-Nyhan syndrome details
BloodDetected and Quantified4.23 +/- 1.92 uMAdult (>18 years old)BothCanavan disease details
Cerebrospinal Fluid (CSF)Detected and Quantified2.30 (1.90-2.70) uMAdult (>18 years old)BothDegenerative disc disease details
Associated Disorders and Diseases
Disease References
Canavan disease
  1. 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
  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
Lesch-Nyhan syndrome
  1. 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)Download (PDF)
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

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
Adenosine triphosphate + Uridine → ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine → Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine → Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine → IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine → dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine → dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine → dUDP + Uridine 5'-monophosphatedetails
General function:
Involved in RNA binding
Specific function:
Converts specific uridines to PSI in a number of tRNA substrates. Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA. Involved in regulation of nuclear receptor activity possibly through pseudouridylation of SRA1 RNA
Gene Name:
PUS1
Uniprot ID:
Q9Y606
Molecular weight:
47469.7
General function:
Involved in RNA processing
Specific function:
Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme
Gene Name:
DKC1
Uniprot ID:
O60832
Molecular weight:
57673.7
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK2
Uniprot ID:
Q9BZX2
Molecular weight:
29298.92
Reactions
Adenosine triphosphate + Uridine → ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine → Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine → Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine → IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine → dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine → dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine → dUDP + Uridine 5'-monophosphatedetails
General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
AID
Uniprot ID:
Q546Y9
Molecular weight:
23953.3
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
Uridine 5'-monophosphate + Water → Uridine + Phosphoric aciddetails
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:
CDA
Uniprot ID:
P32320
Molecular weight:
16184.545
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
UPP1
Uniprot ID:
Q16831
Molecular weight:
33934.005
Reactions
Uridine + Phosphoric acid → Uracil + Ribose 1-phosphatedetails
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis. Shows substrate specificity and accept uridine, deoxyuridine, and thymidine as well as the two pyrimidine nucleoside analogs 5-fluorouridine and 5-fluoro-2(')-deoxyuridine as substrates.
Gene Name:
UPP2
Uniprot ID:
O95045
Molecular weight:
41601.795
Reactions
Uridine + Phosphoric acid → Uracil + Ribose 1-phosphatedetails
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
Reactions
Adenosine triphosphate + Uridine → ADP + Uridine 5'-monophosphatedetails
Uridine triphosphate + Uridine → Uridine 5'-diphosphate + Uridine 5'-monophosphatedetails
Guanosine triphosphate + Uridine → Guanosine diphosphate + Uridine 5'-monophosphatedetails
Inosine triphosphate + Uridine → IDP + Uridine 5'-monophosphatedetails
Deoxyadenosine triphosphate + Uridine → dADP + Uridine 5'-monophosphatedetails
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
Thymidine 5'-triphosphate + Uridine → dTDP + Uridine 5'-monophosphatedetails
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Uridine → dUDP + Uridine 5'-monophosphatedetails
General function:
Involved in RNA binding
Specific function:
Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death
Gene Name:
PUS10
Uniprot ID:
Q3MIT2
Molecular weight:
60243.7
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at position 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
Q9BZE2
Molecular weight:
55647.0
General function:
Involved in RNA binding
Specific function:
tRNA uridine = tRNA pseudouridine
Gene Name:
PUSL1
Uniprot ID:
Q8N0Z8
Molecular weight:
33232.5
General function:
Involved in zinc ion binding
Specific function:
DNA cytidine deaminase which may provide cellular innate resistance to a specific panel of genetic invaders including endogenous retroelements and a subset of viruses.
Gene Name:
APOBEC3H
Uniprot ID:
Q6NTF7
Molecular weight:
21529.795
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Single-stranded DNA cytidine deaminase involved in foreign DNA clearance. May trigger C-to-U hypermutation in exogenous DNA leading to its degradation. Provides cellular innate resistance to a specific panel of genetic invaders including endogenous retroelements and a subset of viruses. May have a preference for cytidines in a C-C sequence context. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.
Gene Name:
APOBEC3A
Uniprot ID:
P31941
Molecular weight:
23011.83
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Probable DNA cytidine deaminase involved in foreign DNA clearance. May provide cellular innate resistance to a specific panel of genetic invaders including endogenous retroelements and a subset of viruses. Binds to apoB and AU-rich RNAs.
Gene Name:
APOBEC3B
Uniprot ID:
Q9UH17
Molecular weight:
43107.7
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Host cellular restriction factor that may have antiviral activities against exogenous and endogenous viruses, as well as retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.
Gene Name:
APOBEC3C
Uniprot ID:
Q9NRW3
Molecular weight:
22825.725
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Probable DNA cytidine deaminase involved in foreign DNA clearance. May provide cellular innate resistance to a specific panel of genetic invaders including endogenous retroelements and a subset of viruses.
Gene Name:
APOBEC3D
Uniprot ID:
Q96AK3
Molecular weight:
46598.035
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Host cellular restriction factor that may have antiviral activities against exogenous and endogenous viruses, as well as retrotransposons. After being packaged into HIV-1 virions, blocks productive infection by massively editing dC residues to dU on the DNA minus strand during reverse transcription. The editing of the minus strand DNA of HIV-1 during reverse transcription leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.
Gene Name:
APOBEC3F
Uniprot ID:
Q8IUX4
Molecular weight:
11822.52
Reactions
Cytidine + Water → Uridine + Ammoniadetails
General function:
Not Available
Specific function:
Single-stranded DNA-specific cytidine deaminase. Involved in somatic hypermutation, gene conversion, and class-switch recombination in B-lymphocytes. Required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.
Gene Name:
AICDA
Uniprot ID:
Q9GZX7
Molecular weight:
23953.265
Reactions
Cytidine + Water → Uridine + Ammoniadetails