Showing Compound 5-Hydroxymethyluracil (FDB022061)

Record Information

Version

1.0

Creation date

2011-09-21 00:07:48 UTC

Update date

2019-11-26 03:21:01 UTC

Primary ID

FDB022061

Secondary Accession Numbers

Not Available

Chemical Information

FooDB Name

5-Hydroxymethyluracil

Description

5-Hydroxymethyluracil, also known as a-hydroxythymine, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 5-Hydroxymethyluracil has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make 5-hydroxymethyluracil a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 5-Hydroxymethyluracil.

CAS Number

4433-40-3

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	Source
5-(Hydroxymethyl)-2,4(1H,3H)-pyrimidinedione	ChEBI
5-(Hydroxymethyl)uracil	ChEBI
5-HYDROXYMETHYL uracil	ChEBI
5-(Hydroxymethyl)-1,3-dihydropyrimidine-2,4-dione	HMDB
a-Hydroxythymine	HMDB
alpha-Hydroxythymine	HMDB
Hydroxymethyluracil	HMDB
5-Hydroxymethyluracil	hmdb

Predicted Properties

Property	Value	Source
Water Solubility	14 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-1.7	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	8.68	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.43 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	32.1 m³·mol⁻¹	ChemAxon
Polarizability	12.34 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C5H6N2O3

IUPAC name

5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione

InChI Identifier

InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)

InChI Key

JDBGXEHEIRGOBU-UHFFFAOYSA-N

Isomeric SMILES

OCC1=CNC(=O)NC1=O

Average Molecular Weight

142.1127

Monoisotopic Molecular Weight

142.037842068

Classification

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Hydropyrimidine
Vinylogous amide
Heteroaromatic compound
Lactam
Urea
Azacycle
Alcohol
Hydrocarbon derivative
Aromatic alcohol
Organic oxide
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidone (CHEBI:16964 )
primary alcohol (CHEBI:16964 )
a small molecule (CPD-254 )

Ontology

Physiological effect

Health effect:

Health condition:

Thymidine treatment

Disposition

Source:

Endogenous

Biological location:

Subcellular:

Cytoplasm

Biofluid and excreta:

Physico-Chemical Properties

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Solid
Physical Description	Not Available
Mass Composition	Not Available
Melting Point	Not Available
Boiling Point	Not Available
Experimental Water Solubility	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Isoelectric point	Not Available
Charge	Not Available
Optical Rotation	Not Available
Spectroscopic UV Data	Not Available
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	5-Hydroxymethyluracil, non-derivatized, GC-MS Spectrum	splash10-0a4i-0923000000-56a7dc66579bc2dd485b	Spectrum
GC-MS	5-Hydroxymethyluracil, non-derivatized, GC-MS Spectrum	splash10-0a4i-0923000000-56a7dc66579bc2dd485b	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-03kc-4900000000-1cac35d0ba0cca9e8da8	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00di-5910000000-e4ecb5b2c252b1dd98a6	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	5-Hydroxymethyluracil, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00di-3900000000-5914a7f193ef00b46813	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0f89-9000000000-baed63743f1c3f212a8c	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0pc0-9000000000-0ff7e6cec32d4f6a93ce	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - , negative	splash10-0006-1900000000-c15a268f199a45782f94	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9200000000-37d9ec4a1e994196876b	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-743c2de03cb5f65bb458	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0006-1900000000-9692a096d1a7d0bb32c8	2021-09-20	View Spectrum
MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0006-7900000000-ebcc62da3f6c16c368f9	2021-09-20	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004l-0900000000-4db52d8921bc6b9e27d9	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-6900000000-74ddd3dbfd8e6a457bee	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000t-9100000000-b418e2767863592cb8de	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-2900000000-5c173dfa10b778d98c52	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9500000000-b46a4f1e0f9872c639de	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-6613bb83bb842d70dfc0	2017-09-01	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-c9b85bee66bc9b6f7fa5	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-5900000000-fb2fe160d3fd7a32fbfc	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05fr-9000000000-0e50a0012c8e06917b1a	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-006x-1900000000-972ab29c67e5ac9b7102	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dl-8900000000-e306682075b170218ba8	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-e3c2901699c5071255a0	2021-09-24	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum