Bovine Metabolome Database: Showing metabocard for Ribothymidine (BMDB0000884)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:38:03 UTC

Update Date

2020-05-11 20:38:11 UTC

BMDB ID

BMDB0000884

Secondary Accession Numbers

BMDB00884

Metabolite Identification

Common Name

Ribothymidine

Description

Ribothymidine, also known as 5-methyl-uridine or thymine riboside, 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. Ribothymidine exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Ribothymidine exists in all living organisms, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-(beta-D-Ribofuranosyl)thymine	ChEBI
Ribosylthymidine	ChEBI
t	ChEBI
Thymine riboside	ChEBI
1-(b-D-Ribofuranosyl)thymine	Generator
1-(Β-D-ribofuranosyl)thymine	Generator
1-b-D-Ribofuranosylthymine	HMDB
1-beta-delta-Ribofuranosylthymine	HMDB
5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedione	HMDB
5-Methyl-uridine	HMDB
5-Methyluridine	HMDB
b-D-Ribofuranoside thymine-1	HMDB
beta-D-Ribofuranoside	HMDB
beta-delta-Ribofuranoside	HMDB
beta-delta-Ribofuranoside thymine-1	HMDB
Ribosylthymine	HMDB
Thymine ribofuranoside	HMDB
Thymine ribonucleoside	HMDB
Thymine-1 beta-D-ribofuranosylthymine	HMDB
Thymine-1 beta-delta-ribofuranosylthymine	HMDB

Chemical Formula

C₁₀H₁₄N₂O₆

Average Molecular Weight

258.228

Monoisotopic Molecular Weight

258.08518619

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

thymidin

CAS Registry Number

1463-10-1

SMILES

CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1

InChI Key

DWRXFEITVBNRMK-JXOAFFINSA-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

methyluridine (CHEBI:45996 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	183 - 187 °C	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	-1.7	ALOGPS
logP	-2	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	9.95	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	56.92 m³·mol⁻¹	ChemAxon
Polarizability	24.1 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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bf-9420000000-897dab8f4bbf7b8e664c	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0kp0-6879400000-656a0a43be4a2cd044e7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-1653ad80c56ae3727f92	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-2900000000-826774188d3e78ca38f2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a6r-9800000000-f5daf31a98b364b70f8c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0090000000-f186cfbb52edc03ff4de	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-004i-0900000000-9f7398feab5dd8950264	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-893019db60499c0a9602	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-004i-2900000000-461a9c94bf89e5b47970	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-1db6a34eff49b044d944	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-004i-1900000000-1c2ee21cd9d3515f7124	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1970000000-ba6f9aa1164c365abfa2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-01u0-8900000000-a63ffd4c990b9c9a543a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-71ebad0df798bf2ac282	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-06w9-8900000000-3c0ceb68319de86fc30f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-004i-1900000000-45b9a7b5e831351a1fe0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-e1eddf8b44309a38eebb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0910000000-90f6da130f49fa9df29d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-5900000000-203a4367756530615ffd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004j-9800000000-13e51659da01285bdc7f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6r-1490000000-4ba707a2228996f9f9f7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-6920000000-a25c60ade61d6d32f0f1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001m-9100000000-37e601ae2d82d72111e7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-f08754aed5978a645b7c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3910000000-01ae005a14dd4c188d46	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9700000000-513e87b6fba58d79ef98	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-0950000000-b4a8bf9fcddaedc20b74	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Milk
Placenta
Semen

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 29291809	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Semen	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 29634739	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000884

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022298

KNApSAcK ID

Not Available

Chemspider ID

393058

KEGG Compound ID

Not Available

BioCyc ID

CPD-15123

BiGG ID

Not Available

Wikipedia Link

5-methyluridine

METLIN ID

5843

PubChem Compound

445408

PDB ID

Not Available

ChEBI ID

45996

References

Synthesis Reference

Maruyama, Shogo; Kumon, Satoru. 5-Methyluridine manufacture with microorganism. Jpn. Kokai Tokkyo Koho (1996), 6 pp.

Material Safety Data Sheet (MSDS)

Not Available

General References

Mung D, Li L: Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk. Anal Chim Acta. 2018 Feb 25;1001:78-85. doi: 10.1016/j.aca.2017.11.019. Epub 2017 Nov 14. [PubMed:29291809 ]

Showing metabocard for Ribothymidine (BMDB0000884)

Structure for BMDB0000884 (Ribothymidine)