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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:53 UTC
HMDB IDHMDB0000296
Secondary Accession Numbers
  • HMDB00296
Metabolite Identification
Common NameUridine
Description
Structure
Thumb
Synonyms
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
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Urea
  • Secondary alcohol
  • Lactam
  • Organoheterocyclic compound
  • Oxacycle
  • Azacycle
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary alcohol
  • Alcohol
  • Organic oxygen compound
  • Organic oxide
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Disposition
Biological locationSource
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point163 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.98HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Astarita_neg145.730932474
[M-H]-Baker154.13330932474
[M-H]-MetCCS_test_neg148.230932474
[M+H]+Astarita_pos151.730932474
[M-H]-Not Available151.2http://allccs.zhulab.cn/database/detail?ID=AllCCS00000155
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biospecimen Locations
  • Blood
  • Breast Milk
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
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 ]
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 ]
Colorectal cancer
  1. Qiu Y, Cai G, Su M, Chen T, Zheng X, Xu Y, Ni Y, Zhao A, Xu LX, Cai S, Jia W: Serum metabolite profiling of human colorectal cancer using GC-TOFMS and UPLC-QTOFMS. J Proteome Res. 2009 Oct;8(10):4844-50. doi: 10.1021/pr9004162. [PubMed:19678709 ]
  2. Ni Y, Xie G, Jia W: Metabonomics of human colorectal cancer: new approaches for early diagnosis and biomarker discovery. J Proteome Res. 2014 Sep 5;13(9):3857-70. doi: 10.1021/pr500443c. Epub 2014 Aug 14. [PubMed:25105552 ]
  3. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  4. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  5. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Uremia
  1. Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
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 ]
Irritable bowel syndrome
  1. Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ]
Ulcerative colitis
  1. Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res. 2011 Sep 2;10(9):4208-18. doi: 10.1021/pr2003598. Epub 2011 Aug 8. [PubMed:21761941 ]
Argininemia
  1. Naylor EW, Cederbaum SD: Urinary pyrimidine excretion in arginase deficiency. J Inherit Metab Dis. 1981;4(4):207-10. [PubMed:6796772 ]
Associated OMIM IDs
DrugBank IDDB02745
Phenol Explorer Compound IDNot Available
FooDB IDFDB007411
KNApSAcK IDC00019674
Chemspider ID5807
KEGG Compound IDC00299
BioCyc IDURIDINE
BiGG ID34541
Wikipedia LinkUridine
METLIN ID90
PubChem Compound6029
PDB IDNot Available
ChEBI ID16704
Food Biomarker OntologyNot Available
VMH IDURI
MarkerDB IDMDB00029980
Good Scents IDNot Available
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 ]
  3. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Only showing the first 10 proteins. There are 26 proteins in total.

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 + Phosphatedetails
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 + Phosphatedetails
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 + Phosphatedetails
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 + Phosphatedetails
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 + Phosphatedetails
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

Only showing the first 10 proteins. There are 26 proteins in total.