Human Metabolome Database Version 3.5

Showing metabocard for Uridine (HMDB00296)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:16 -0700
HMDB ID HMDB00296
Secondary Accession Numbers None
Metabolite Identification
Common Name Uridine
Description Uridine 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C9H12N2O6
Average Molecular Weight 244.2014
Monoisotopic Molecular Weight 244.069536126
IUPAC Name 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name uridine
CAS Registry Number 58-96-8
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 Key DRTQHJPVMGBUCF-XVFCMESISA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleosides and Analogues
Sub Class N/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 Parent Pyrimidine Nucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 163 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP -1.98 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 135 g/L ALOGPS
LogP -1.84 ALOGPS
LogP -2.4 ChemAxon
LogS -0.26 ALOGPS
pKa (strongest acidic) 9.7 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 6 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 119.33 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 52.57 ChemAxon
Polarizability 21.78 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
13C NMR Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
MS/MS Spectrum LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
3.10 (2.90-3.30) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
3.12 +/- 1.31 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.22 +/- 0.07 umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected and Quantified
0.21 +/- 0.08 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.21 +/- 0.09 umol/mmol creatinine Adult (>18 years old) Female Normal
Urine Detected and Quantified
0.994 (0.637-1.351) umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 7.7 +/- 0.9 uM Adult (>18 years old) Both Lesch-Nyhan syndrome
Blood Detected and Quantified 4.23 +/- 1.92 uM Adult (>18 years old) Both Canavan disease
Cerebrospinal Fluid (CSF) Detected and Quantified 2.30 (1.90-2.70) uM Adult (>18 years old) Both Degenerative disc disease
Associated Disorders and Diseases
Disease References
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 Link_out
      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 Link_out
          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 Link_out
              Associated OMIM IDs
              DrugBank ID DB02745 Link_out
              DrugBank Metabolite ID Not Available
              Phenol Explorer Compound ID Not Available
              Phenol Explorer Metabolite ID Not Available
              FoodDB ID FDB007411
              KNApSAcK ID C00019674 Link_out
              Chemspider ID 5807 Link_out
              KEGG Compound ID C00299 Link_out
              BioCyc ID URIDINE Link_out
              BiGG ID 34541 Link_out
              Wikipedia Link Uridine Link_out
              NuGOwiki Link HMDB00296 Link_out
              Metagene Link HMDB00296 Link_out
              METLIN ID 90 Link_out
              PubChem Compound 6029 Link_out
              PDB ID URI Link_out
              ChEBI ID 16704 Link_out
              References
              Synthesis Reference Doi, 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. 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 Link_out
              2. 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 Link_out

              Enzymes
              Name: 5'-nucleotidase
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5E
              Uniprot ID: P21589 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Cytosolic 5'-nucleotidase 1B
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5C1B
              Uniprot ID: Q96P26 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Cytosolic 5'-nucleotidase 1A
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5C1A
              Uniprot ID: Q9BXI3 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: 5'(3')-deoxyribonucleotidase, cytosolic type
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5C
              Uniprot ID: Q8TCD5 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: 5'(3')-deoxyribonucleotidase, mitochondrial
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5M
              Uniprot ID: Q9NPB1 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Uridine-cytidine kinase 1
              Reactions:
              Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphate details
              Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphate details
              Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphate details
              Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphate details
              Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphate details
              dGTP + Uridine unknown dGDP + Uridine 5'-monophosphate details
              Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphate details
              dCTP + Uridine unknown dCDP + Uridine 5'-monophosphate details
              Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphate details
              Gene Name: UCK1
              Uniprot ID: Q9HA47 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: tRNA pseudouridine synthase A, mitochondrial
              Reactions: Not Available
              Gene Name: PUS1
              Uniprot ID: Q9Y606 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: H/ACA ribonucleoprotein complex subunit 4
              Reactions: Not Available
              Gene Name: DKC1
              Uniprot ID: O60832 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Uridine-cytidine kinase 2
              Reactions:
              Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphate details
              Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphate details
              Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphate details
              Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphate details
              Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphate details
              dGTP + Uridine unknown dGDP + Uridine 5'-monophosphate details
              Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphate details
              dCTP + Uridine unknown dCDP + Uridine 5'-monophosphate details
              Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphate details
              Gene Name: UCK2
              Uniprot ID: Q9BZX2 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: AID
              Reactions: Not Available
              Gene Name: AID
              Uniprot ID: Q546Y9 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Cytosolic 5'-nucleotidase 3
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5C3
              Uniprot ID: Q9H0P0 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Cytosolic purine 5'-nucleotidase
              Reactions:
              Uridine 5'-monophosphate + Water unknown Uridine + Phosphoric acid details
              Gene Name: NT5C2
              Uniprot ID: P49902 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Cytidine deaminase
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: CDA
              Uniprot ID: P32320 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Uridine phosphorylase 1
              Reactions:
              Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphate details
              Gene Name: UPP1
              Uniprot ID: Q16831 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Uridine phosphorylase 2
              Reactions:
              Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphate details
              Gene Name: UPP2
              Uniprot ID: O95045 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Uridine-cytidine kinase-like 1
              Reactions:
              Adenosine triphosphate + Uridine unknown ADP + Uridine 5'-monophosphate details
              Uridine triphosphate + Uridine unknown Uridine 5'-diphosphate + Uridine 5'-monophosphate details
              Guanosine triphosphate + Uridine unknown Guanosine diphosphate + Uridine 5'-monophosphate details
              Inosine triphosphate + Uridine unknown IDP + Uridine 5'-monophosphate details
              Deoxyadenosine triphosphate + Uridine unknown dADP + Uridine 5'-monophosphate details
              dGTP + Uridine unknown dGDP + Uridine 5'-monophosphate details
              Thymidine 5'-triphosphate + Uridine unknown dTDP + Uridine 5'-monophosphate details
              dCTP + Uridine unknown dCDP + Uridine 5'-monophosphate details
              Deoxyuridine triphosphate + Uridine unknown dUDP + Uridine 5'-monophosphate details
              Gene Name: UCKL1
              Uniprot ID: Q9NWZ5 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Putative tRNA pseudouridine synthase Pus10
              Reactions: Not Available
              Gene Name: PUS10
              Uniprot ID: Q3MIT2 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: tRNA pseudouridine synthase 3
              Reactions: Not Available
              Gene Name: PUS3
              Uniprot ID: Q9BZE2 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: tRNA pseudouridine synthase-like 1
              Reactions: Not Available
              Gene Name: PUSL1
              Uniprot ID: Q8N0Z8 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: DNA dC->dU-editing enzyme APOBEC-3H
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3H
              Uniprot ID: Q6NTF7 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Probable DNA dC->dU-editing enzyme APOBEC-3A
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3A
              Uniprot ID: P31941 Link_out
              Protein Sequence: FASTA
              Name: Probable DNA dC->dU-editing enzyme APOBEC-3B
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3B
              Uniprot ID: Q9UH17 Link_out
              Protein Sequence: FASTA
              Name: Probable DNA dC->dU-editing enzyme APOBEC-3C
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3C
              Uniprot ID: Q9NRW3 Link_out
              Protein Sequence: FASTA
              Name: Probable DNA dC->dU-editing enzyme APOBEC-3D
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3D
              Uniprot ID: Q96AK3 Link_out
              Protein Sequence: FASTA
              Name: DNA dC->dU-editing enzyme APOBEC-3F
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: APOBEC3F
              Uniprot ID: Q8IUX4 Link_out
              Protein Sequence: FASTA
              Name: Activation-induced cytidine deaminase
              Reactions:
              Cytidine + Water unknown Uridine + Ammonia details
              Gene Name: AICDA
              Uniprot ID: Q9GZX7 Link_out
              Protein Sequence: FASTA