Livestock Metabolome Database: Showing metabocard for Uridine (LMDB00132)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:43:03 UTC

Update Date

2016-07-20 21:03:28 UTC

Lmdb

LMDB00132

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Uridine

Description

Uridine, 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.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-beta-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione	ChEBI
1-beta-D-Ribofuranosyluracil	ChEBI
beta-Uridine	ChEBI
u	ChEBI
Urd	ChEBI
Uridin	ChEBI
1-b-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione	Generator
1-Β-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione	Generator
1-b-D-Ribofuranosyluracil	Generator
1-Β-D-ribofuranosyluracil	Generator
b-Uridine	Generator
Β-uridine	Generator
1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-beta-delta-Ribofuranosyluracil	HMDB
b-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1	HMDB
beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1	HMDB
Allo uridine	HMDB
Allo-uridine	HMDB
Allouridine	HMDB

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 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

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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

uridines (CHEBI:16704 )
Ribonucleosides (C00299 )

Ontology

Status

Detected but not Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.8	ALOGPS
logP	-2.4	ChemAxon
logS	-0.26	ALOGPS
pKa (Strongest Acidic)	9.7	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	119.33 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.57 m³·mol⁻¹	ChemAxon
Polarizability	21.81 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-00kb-1970000000-d1bfa838a4e9fa77c862	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00kb-1960000000-a8283468b762a8520102	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-014i-1950000000-70fdf4785544d0968f70	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (3 TMS)	splash10-00di-9520000000-591c0bcf8f956d710367	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-066s-2970000000-36fbef6f6b10c2895df4	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-014i-1890000000-dd0569d4351a64c566c9	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00kb-1970000000-d1bfa838a4e9fa77c862	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00kb-1960000000-a8283468b762a8520102	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-1950000000-70fdf4785544d0968f70	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9520000000-591c0bcf8f956d710367	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-066s-2970000000-36fbef6f6b10c2895df4	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-014i-1890000000-dd0569d4351a64c566c9	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1940000000-8b7a5ce66afa9b9bf939	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00kb-1950000000-00519445de22f955367d	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-056u-9530000000-e83d5f042dbda82911cf	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0g30-5935200000-88c9a24e13b0f41cbc83	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-03di-0900000000-7010b37007f5c3d9ce1f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-3900000000-b4639c8c89eac6158da6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-022a-9200000000-f8472930d09b32f54790	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0291000000-aebaa77a411473acb859	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014j-9000000000-205562662b564ebdca28	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-776595fd1c19f6ec51cd	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-000i-0900000000-10358e53c56bcb50ed4c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0002-0971000000-f989283d2dec564a3af0	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00kf-9000000000-c11e7bfdec0b5c7bf450	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-000i-9000000000-104e62fbffc4110779ef	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-03di-0900000000-eaf6ff9ac3971d6f045f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-052f-0697120000-c9fd5b8d641165d84e92	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-9000000000-995de18be458c48a8d2d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0udi-0590000000-4d1d6aba25697dd11da8	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0uki-0190000000-3aea11527d0520158d77	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004l-0291010000-c8f22405e9290fccc011	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0udi-0490000000-1a2f990a874bb1868249	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-0090000000-c8efbe58f0df63698b2c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0006-0090000000-7495d9b948a8e3b7b83b	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-03dj-3960000000-3466ccfdf88139ddf140	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-03di-3900000000-0d08e4a7d4b8aacee6e6	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-03di-4900000000-d942ee27b3ca1d6ef94d	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-03di-9700000000-594c7bb6dc6de848ff11	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-022d-9100000000-2826c4eb794745ec3148	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-03di-0910000000-617b4ec6cf749942c0cd	Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-08mi-9400000000-bafe048989f1a5c86d2d	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Colostrum
Feces
Meat
Milk
Synovial Fluid
Urine

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Colostrum	Detected but not Quantified	Not Applicable	Not Available	Bovine	25637742	details
Feces	Detected but not Quantified	Not Applicable	Not Available	Equine	E. E. Escalona, J...	details
Meat	Detected but not Quantified	Not Applicable	Not Available	Bovine	25637742	details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	Kurt J. Boudonck,...	details
Synovial Fluid	Detected but not Quantified	Not Applicable	Not Available	Ovine	25283885	details
Urine	Detected but not Quantified	Not Applicable	Not Available	Bovine	22059599	details
Urine	Detected but not Quantified	Not Applicable	Not Available	Porcine	21761043	details