Bovine Metabolome Database: Showing metabocard for Thymidine (BMDB0000273)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:27:43 UTC

Update Date

2020-05-21 16:29:01 UTC

BMDB ID

BMDB0000273

Secondary Accession Numbers

BMDB00273

Metabolite Identification

Common Name

Thymidine

Description

Thymidine, also known as deoxythymidine or DTHD, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Thymidine is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Thymidine exists in all living species, ranging from bacteria to humans. Thymidine participates in a number of enzymatic reactions, within cattle. In particular, Thymidine can be biosynthesized from 5-thymidylic acid through its interaction with the enzyme cytosolic purine 5'-nucleotidase. In addition, Thymidine can be converted into 5-thymidylic acid; which is catalyzed by the enzyme thymidine kinase, cytosolic. In cattle, thymidine is involved in the metabolic pathway called the pyrimidine metabolism pathway. Thymidine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione	ChEBI
2'-Deoxy-5-methyluridine	ChEBI
2'-Deoxythymidine	ChEBI
2'-Thymidine	ChEBI
5-Methyl-2'-deoxyuridine	ChEBI
Deoxythymidine	ChEBI
DTHD	ChEBI
T	ChEBI
Thymine 2'-deoxyriboside	ChEBI
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione	Generator
1-(2-Deoxy-β-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione	Generator
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione	HMDB
1-[4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione	HMDB
2'-Deoxy-5-methyl-uridine	HMDB
5-Methyldeoxyuridine	HMDB
Deoxyribothymidine	HMDB
DT	HMDB
DThyd	HMDB
Thymidin	HMDB
Thymine 2-desoxyriboside	HMDB
Thymine deoxyriboside	HMDB
Thymine-1 2-deoxy-b-D-ribofuranoside	HMDB
Thymine-1 2-deoxy-beta-delta-ribofuranoside	HMDB
2' Deoxythymidine	HMDB

Chemical Formula

C₁₀H₁₄N₂O₅

Average Molecular Weight

242.2286

Monoisotopic Molecular Weight

242.090271568

IUPAC Name

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

Traditional Name

thymidine

CAS Registry Number

50-89-5

SMILES

CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O

InChI Identifier

InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1

InChI Key

IQFYYKKMVGJFEH-XLPZGREQSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Pyrimidone
Hydroxypyrimidine
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside (CHEBI:17748 )
Deoxyribonucleosides (C00214 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Lysosome
Mitochondria

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	73.5 mg/mL	Not Available
LogP	-0.93	SANGSTER (1993)

Predicted Properties

Property	Value	Source
logP	-1.3	ALOGPS
logP	-1.1	ChemAxon
logS	-0.56	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.1 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.41 m³·mol⁻¹	ChemAxon
Polarizability	23.06 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
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0udi-1900000000-8e769118bc877facb05f	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0ue9-2910000000-823bcee487948a9c786f	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-1900000000-8e769118bc877facb05f	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0ue9-2910000000-823bcee487948a9c786f	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0900000000-996530d1ea081ac2a7c7	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0l6r-0900000000-4645a52830204c8ef5d0	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0zfr-0900000000-76b8a050c10b514ed50b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9530000000-627a60bbe3e0b90f58cb	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0g4i-7905000000-7b0c67709e3a5f91841a	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_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 (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_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
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-004i-0900000000-1c2ba2f2aace4a76cdea	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-004i-3900000000-d177672ef3f383adbb5d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-01p9-9000000000-4483af567feecb34a651	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-0006-0090000000-435be9f03e969dbabb79	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0006-5690000000-79b230d52929aa67bbf2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0006-9100000000-28a604508965067c85c5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-0006-9000000000-360e0667ff3d7d77e706	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0006-9000000000-b1fecd2d1fa166e22d5f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-004i-1920000000-1a2e609b8a19ef491964	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-004i-1900000000-5e4a733641fa285e7f74	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-004i-3900000000-f734d5813fecb7a31814	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-01t9-5900000000-53b0016c66aa014c2abc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-03e9-9600000000-48f1a0d5512651a93e14	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-004i-1910000000-f02c2133ea475f4f838c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-08i0-2900000000-ec21970768da0fbf8ce5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-0002-9000000000-17c234cb0e8de5ae82f4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-014i-9000000000-d7e5ed251a93758682ec	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-0090000000-435be9f03e969dbabb79	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0006-5690000000-79b230d52929aa67bbf2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-9ad72ff6cb2e2dfab911	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4900000000-3b1e6c50c2450e123648	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-6900000000-d30b05dfe1b6d25ebd2b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-052g-1940000000-ce16baa1ceb8a83565c2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufr-3920000000-c6ff3f238b6fed007635	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-104a4f5a4fe8a0ed5ca3	View in MoNA
MS	Mass Spectrum (Electron Ionization)	splash10-01dj-9300000000-6e24b5b6d36e07dd73d0	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, D₂O, 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, 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
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
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	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
Lysosome
Mitochondria

Biospecimen Locations

Adipose Tissue
Adrenal Gland
Bladder
Epidermis
Fibroblasts
Intestine
Kidney
Liver
Milk
Neuron
Pancreas
Placenta
Platelet
Prostate Tissue
Skeletal Muscle
Spleen
Testis
Thyroid Gland

Pathways

Name	SMPDB/Pathwhiz	KEGG
Pyrimidine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Adipose Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Adrenal Gland	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Bladder	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 29565828	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Thyroid Gland	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000273

DrugBank ID

DB04485

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17748

References

Synthesis Reference

Herdewijn, P.; Kerremans, L.; Wigerinck, P.; Vandendriessche, F.; Van Aerschot, A. Synthesis of thymidine from 5-iodo-2'-deoxyuridine. Tetrahedron Letters (1991), 32(34), 4397-400.

Material Safety Data Sheet (MSDS)

Not Available

General References

Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details

1. Cytosolic purine 5'-nucleotidase

General function:: Involved in 5'-nucleotidase activity
Specific function:: May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:: NT5C2
Uniprot ID:: O46411
Molecular weight:: 64841.0

Reactions

5-Thymidylic acid + Water → Thymidine + Hydrogen phosphate	details

Enzyme Details

2. Thymidine kinase, cytosolic

General function:: Not Available
Specific function:: Not Available
Gene Name:: TK1
Uniprot ID:: A5D7R8
Molecular weight:: 26377.0

Reactions

Thymidine + Adenosine triphosphate → 5-Thymidylic acid + ADP	details

Showing metabocard for Thymidine (BMDB0000273)

Structure for BMDB0000273 (Thymidine)

Enzymes

Reactions

Reactions