Record Information
Version1.0
Created at2020-04-17 18:42:18 UTC
Updated at2020-12-07 19:11:05 UTC
CannabisDB IDCDB004841
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameUridine
DescriptionUridine, also known as beta-uridine or Urd, 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. Uridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine exists in all living species, ranging from bacteria to humans. In humans, uridine is involved in the metabolic disorder called the g(m2)-gangliosidosis: variant b, tay-sachs disease pathway. Uridine, with regard to humans, has been found to be associated with several diseases such as uremia, irritable bowel syndrome, degenerative disc disease, and canavan disease; uridine has also been linked to the inborn metabolic disorder argininemia. A ribonucleoside composed of a molecule of uracil attached to a ribofuranose moiety via a beta-N(1)-glycosidic bond. Uridine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
Synonyms
ValueSource
1-beta-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dioneChEBI
1-beta-D-RibofuranosyluracilChEBI
beta-UridineChEBI
uChEBI
UrdChEBI
UridinChEBI
1-b-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dioneGenerator
1-Β-D-ribofuranosylpyrimidine-2,4(1H,3H)-dioneGenerator
1-b-D-RibofuranosyluracilGenerator
1-Β-D-ribofuranosyluracilGenerator
b-UridineGenerator
Β-uridineGenerator
1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-beta-delta-RibofuranosyluracilHMDB
b-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1HMDB
beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1HMDB
Allo uridineHMDB
Allo-uridineHMDB
AllouridineHMDB
Chemical FormulaC9H12N2O6
Average Molecular Weight244.2
Monoisotopic Molecular Weight244.0695
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 Number68184-15-6
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

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Physical Properties
StateNot Available
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
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.57 m³·mol⁻¹ChemAxon
Polarizability21.81 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
EI-MSMass Spectrum (Electron Ionization)splash10-08mi-9400000000-bafe048989f1a5c86d2dSpectrum
GC-MSUridine, 3 TMS, GC-MS Spectrumsplash10-00kb-1970000000-d1bfa838a4e9fa77c862Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-00kb-1960000000-a8283468b762a8520102Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-014i-1950000000-70fdf4785544d0968f70Spectrum
GC-MSUridine, 3 TMS, GC-MS Spectrumsplash10-00di-9520000000-591c0bcf8f956d710367Spectrum
GC-MSUridine, 4 TMS, GC-MS Spectrumsplash10-066s-2970000000-36fbef6f6b10c2895df4Spectrum
GC-MSUridine, 3 TMS, GC-MS Spectrumsplash10-014i-1890000000-dd0569d4351a64c566c9Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-00kb-1970000000-d1bfa838a4e9fa77c862Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-00kb-1960000000-a8283468b762a8520102Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-014i-1950000000-70fdf4785544d0968f70Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-00di-9520000000-591c0bcf8f956d710367Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-066s-2970000000-36fbef6f6b10c2895df4Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-014i-1890000000-dd0569d4351a64c566c9Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-014j-1940000000-8b7a5ce66afa9b9bf939Spectrum
GC-MSUridine, non-derivatized, GC-MS Spectrumsplash10-00kb-1950000000-00519445de22f955367dSpectrum
Predicted GC-MSUridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-056u-9530000000-e83d5f042dbda82911cfSpectrum
Predicted GC-MSUridine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0g30-5935200000-88c9a24e13b0f41cbc83Spectrum
Predicted GC-MSUridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSUridine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-0900000000-7010b37007f5c3d9ce1fSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-3900000000-b4639c8c89eac6158da6Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-022a-9200000000-f8472930d09b32f54790Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-0291000000-aebaa77a411473acb859Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014j-9000000000-205562662b564ebdca28Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-776595fd1c19f6ec51cdSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-000i-0900000000-10358e53c56bcb50ed4cSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0002-0971000000-f989283d2dec564a3af0Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00kf-9000000000-c11e7bfdec0b5c7bf450Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-000i-9000000000-104e62fbffc4110779efSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-03di-0900000000-eaf6ff9ac3971d6f045fSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-052f-0697120000-c9fd5b8d641165d84e92Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-9000000000-995de18be458c48a8d2dSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0udi-0590000000-4d1d6aba25697dd11da8Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0uki-0190000000-3aea11527d0520158d77Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004l-0291010000-c8f22405e9290fccc011Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0udi-0490000000-1a2f990a874bb1868249Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0090000000-c8efbe58f0df63698b2cSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0006-0090000000-7495d9b948a8e3b7b83bSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-03dj-3960000000-3466ccfdf88139ddf140Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-03di-3900000000-0d08e4a7d4b8aacee6e6Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-03di-4900000000-d942ee27b3ca1d6ef94dSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-03di-9700000000-594c7bb6dc6de848ff11Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-022d-9100000000-2826c4eb794745ec3148Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-03di-0910000000-617b4ec6cf749942c0cdSpectrum
NMR
TypeDescriptionView
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
2D NMR[1H,1H] 2D NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
5'-nucleotidaseNT5E6q14-q21P21589 details
Cytosolic 5'-nucleotidase 1BNT5C1B2p24.2Q96P26 details
Cytosolic 5'-nucleotidase 1ANT5C1A1p34.3-p33Q9BXI3 details
5'(3')-deoxyribonucleotidase, cytosolic typeNT5CQ8TCD5 details
5'(3')-deoxyribonucleotidase, mitochondrialNT5MQ9NPB1 details
Uridine-cytidine kinase 1UCK19q34.13Q9HA47 details
tRNA pseudouridine synthase A, mitochondrialPUS112q24.33Q9Y606 details
H/ACA ribonucleoprotein complex subunit 4DKC1O60832 details
Uridine-cytidine kinase 2UCK21q23Q9BZX2 details
AIDAIDQ546Y9 details
Cytosolic 5'-nucleotidase 3NT5C37p14.3Q9H0P0 details
Cytosolic purine 5'-nucleotidaseNT5C210q24.32P49902 details
Cytidine deaminaseCDA1p36.2-p35P32320 details
Uridine phosphorylase 1UPP17p12.3Q16831 details
Uridine phosphorylase 2UPP22q24.1O95045 details
Uridine-cytidine kinase-like 1UCKL120q13.33Q9NWZ5 details
Putative tRNA pseudouridine synthase Pus10PUS102p16.1Q3MIT2 details
tRNA pseudouridine synthase 3PUS311q24.2Q9BZE2 details
tRNA pseudouridine synthase-like 1PUSL11p36.33Q8N0Z8 details
DNA dC->dU-editing enzyme APOBEC-3HAPOBEC3H22q13.1Q6NTF7 details
Activation-induced cytidine deaminaseAICDA12p13Q9GZX7 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
5'-nucleotidaseNT5E6q14-q21P21589 details
Cytosolic 5'-nucleotidase 1BNT5C1B2p24.2Q96P26 details
Cytosolic 5'-nucleotidase 1ANT5C1A1p34.3-p33Q9BXI3 details
5'(3')-deoxyribonucleotidase, cytosolic typeNT5CQ8TCD5 details
5'(3')-deoxyribonucleotidase, mitochondrialNT5MQ9NPB1 details
AIDAIDQ546Y9 details
Cytosolic 5'-nucleotidase 3NT5C37p14.3Q9H0P0 details
Cytosolic purine 5'-nucleotidaseNT5C210q24.32P49902 details
Cytidine deaminaseCDA1p36.2-p35P32320 details
DNA dC->dU-editing enzyme APOBEC-3HAPOBEC3H22q13.1Q6NTF7 details
Probable DNA dC->dU-editing enzyme APOBEC-3AAPOBEC3A22q13.1-q13.2P31941 details
Probable DNA dC->dU-editing enzyme APOBEC-3BAPOBEC3B22q13.1-q13.2Q9UH17 details
Probable DNA dC->dU-editing enzyme APOBEC-3CAPOBEC3C22q13.1Q9NRW3 details
Probable DNA dC->dU-editing enzyme APOBEC-3DAPOBEC3D22q13.1Q96AK3 details
DNA dC->dU-editing enzyme APOBEC-3FAPOBEC3F22q13.1Q8IUX4 details
Activation-induced cytidine deaminaseAICDA12p13Q9GZX7 details
Receptors
Protein NameGene NameLocusUniprot IDDetails
Cytidine deaminaseCDA1p36.2-p35P32320 details
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0000296
DrugBank IDDB02745
Phenol Explorer Compound IDNot Available
FoodDB IDFDB007411
KNApSAcK IDC00019674
Chemspider ID5807
KEGG Compound IDC00299
BioCyc IDURIDINE
BiGG ID34541
Wikipedia LinkUridine
METLIN ID90
PubChem Compound6029
PDB IDNot Available
ChEBI ID16704
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 38 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
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
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
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
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
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
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
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 38 proteins in total.