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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2023-02-21 17:14:52 UTC

HMDB ID

HMDB0000469

Secondary Accession Numbers

HMDB00469

Metabolite Identification

Common Name

5-Hydroxymethyluracil

Description

5-Hydroxymethyluracil (5hmU), also known as alpha-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. 5hmU has been identified as a thymine base modification found in the genomes of a diverse range of organisms (PMID: 28137275 ). 5-hydroxymethyluracil has been detected in bacteriophages, dinoflagellates, leishmania, and in eukaryotic genomes where its level appears to be cell type-specific. 5-Hydroxymethyluracil arises from the oxidation of thymine. 5-Hydroxymethyluracil is produced by the enzyme thymine dioxygenase (EC 1.14.11.6) which catalyzes the chemical reaction thymine + 2-oxoglutarate + O2 <-> 5-hydroxymethyluracil + succinate + CO2. The 3 substrates of this enzyme are thymine, 2-oxoglutarate, and O2, whereas its 3 products are 5-hydroxymethyluracil, succinate, and CO2. The 5hmU base can also be generated by oxidation/hydroxylation of thymine by the Ten-Eleven-Translocation (TET) proteins or result from deamination of 5hmC (PMID: 29184924 ). DNA containing 5hmU has been reported to be more flexible and hydrophilic (PMID: 29184924 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	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

Chemical Formula

C₅H₆N₂O₃

Average Molecular Weight

142.1127

Monoisotopic Molecular Weight

142.037842068

IUPAC Name

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

Traditional Name

5-hydroxymethyluracil

CAS Registry Number

4433-40-3

SMILES

OCC1=CNC(=O)NC1=O

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

Chemical Taxonomy

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

Intervention

Thymidine treatment (HMDB: HMDB0000469)

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 6736109)

Excreta

Biofluid or Excreta

Urine (PMID: 19309105)

Cellular substructure

Cytoplasm (HMDB: HMDB0000469)
Extracellular (HMDB: HMDB0000469)

Source

Endogenous

Endogenous (HMDB: HMDB0000469)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Process

Naturally occurring process

Biological process

Biochemical pathway

Disease pathway

Dihydropyrimidine Dehydrogenase Deficiency (DHPD) (HMDB: HMDB0000469)

Role

Biological role

Human metabolite (HMDB: HMDB0000469)

Industrial application

Pharmaceutical industry

Biomarker

Smoking (MarkerDB: MDB00000168)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	44 mg/mL	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Baker	124.499	30932474
[M-H]-	MetCCS_train_neg	119.208	30932474
[M-H]-	Not Available	121.9	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000325

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	128.127	31661259
DarkChem	[M-H]-	126.326	31661259
AllCCS	[M+H]+	131.365	32859911
AllCCS	[M-H]-	125.691	32859911
DeepCCS	[M+H]+	124.654	30932474
DeepCCS	[M-H]-	121.457	30932474
DeepCCS	[M-2H]-	157.935	30932474
DeepCCS	[M+Na]+	133.211	30932474
AllCCS	[M+H]+	131.4	32859911
AllCCS	[M+H-H2O]+	126.8	32859911
AllCCS	[M+NH4]+	135.6	32859911
AllCCS	[M+Na]+	136.9	32859911
AllCCS	[M-H]-	125.7	32859911
AllCCS	[M+Na-2H]-	127.4	32859911
AllCCS	[M+HCOO]-	129.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.0 minutes	32390414
Predicted by Siyang on May 30, 2022	9.2044 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.65 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	131.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	528.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	332.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	61.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	208.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	49.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	269.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	259.8 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	425.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	594.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	60.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	768.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	212.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	224.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	645.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	264.0 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	323.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxymethyluracil	OCC1=CNC(=O)NC1=O	2638.6	Standard polar	33892256
5-Hydroxymethyluracil	OCC1=CNC(=O)NC1=O	1642.2	Standard non polar	33892256
5-Hydroxymethyluracil	OCC1=CNC(=O)NC1=O	1927.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxymethyluracil,1TMS,isomer #1	C[Si](C)(C)OCC1=C[NH]C(=O)[NH]C1=O	1640.3	Semi standard non polar	33892256
5-Hydroxymethyluracil,1TMS,isomer #2	C[Si](C)(C)N1C=C(CO)C(=O)[NH]C1=O	1661.3	Semi standard non polar	33892256
5-Hydroxymethyluracil,1TMS,isomer #3	C[Si](C)(C)N1C(=O)[NH]C=C(CO)C1=O	1651.3	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1750.4	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	1887.2	Standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)[NH]C1=O	2159.1	Standard polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #2	C[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1738.3	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #2	C[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	1845.3	Standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #2	C[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C)C1=O	2078.8	Standard polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C)C1=O	1731.0	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C)C1=O	1928.9	Standard non polar	33892256
5-Hydroxymethyluracil,2TMS,isomer #3	C[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C)C1=O	2172.2	Standard polar	33892256
5-Hydroxymethyluracil,3TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1897.0	Semi standard non polar	33892256
5-Hydroxymethyluracil,3TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1951.4	Standard non polar	33892256
5-Hydroxymethyluracil,3TMS,isomer #1	C[Si](C)(C)OCC1=CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O	1975.5	Standard polar	33892256
5-Hydroxymethyluracil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=C[NH]C(=O)[NH]C1=O	1907.1	Semi standard non polar	33892256
5-Hydroxymethyluracil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C=C(CO)C(=O)[NH]C1=O	1957.6	Semi standard non polar	33892256
5-Hydroxymethyluracil,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C(=O)[NH]C=C(CO)C1=O	1901.0	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2225.1	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2311.4	Standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)[NH]C1=O	2326.3	Standard polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2174.9	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2271.9	Standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1=C[NH]C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2239.1	Standard polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2234.9	Semi standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2333.4	Standard non polar	33892256
5-Hydroxymethyluracil,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2276.6	Standard polar	33892256
5-Hydroxymethyluracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2453.9	Semi standard non polar	33892256
5-Hydroxymethyluracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2551.9	Standard non polar	33892256
5-Hydroxymethyluracil,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1=CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O	2297.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 5-Hydroxymethyluracil GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0a4i-0923000000-56a7dc66579bc2dd485b	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - 5-Hydroxymethyluracil GC-EI-TOF (Non-derivatized)	splash10-0a4i-0923000000-56a7dc66579bc2dd485b	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (Non-derivatized) - 70eV, Positive	splash10-03kc-4900000000-1cac35d0ba0cca9e8da8	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (1 TMS) - 70eV, Positive	splash10-00di-5910000000-e4ecb5b2c252b1dd98a6	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxymethyluracil GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

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

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	2012-12-04	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected and Quantified	0.12 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	19309105	details
Urine	Detected and Quantified	0.0052 +/- 0.0026 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	15649624	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	88.0 +/- 8.0 uM	Adult (>18 years old)	Both	Solid tumors	6736109	details
Blood	Detected and Quantified	42.0 +/- 21.0 uM	Adult (>18 years old)	Both	Solid tumors	6736109	details
Blood	Detected and Quantified	15.0 +/- 2.0 uM	Adult (>18 years old)	Both	Solid tumors	6736109	details
Blood	Detected and Quantified	63.0 +/- 5.0 uM	Adult (>18 years old)	Both	Solid tumors	6736109	details
Blood	Detected and Quantified	33.0 +/- 4.0 uM	Adult (>18 years old)	Both	Solid tumors	6736109	details
Urine	Detected and Quantified	0.0062 +/- 0.0023 umol/mmol creatinine	Adult (>18 years old)	Both	Smoking	15649624	details

Associated Disorders and Diseases

Disease References

Thymidine treatment
Leyva A, Schornagel JH, Kraal I, Wadman SK, Pinedo HM: Clinical and biochemical studies of high-dose thymidine treatment in patients with solid tumors. J Cancer Res Clin Oncol. 1984;107(3):211-6. [PubMed:6736109 ]
Smoking
Chen HJ, Wu CF, Huang JL: Measurement of urinary excretion of 5-hydroxymethyluracil in human by GC/NICI/MS: correlation with cigarette smoking, urinary TBARS and etheno DNA adduct. Toxicol Lett. 2005 Mar 15;155(3):403-10. [PubMed:15649624 ]

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022061

KNApSAcK ID

Not Available

Chemspider ID

70544

KEGG Compound ID

C03088

BioCyc ID

CPD-254

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5456

PubChem Compound

78168

PDB ID

Not Available

ChEBI ID

16964

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

MDB00000168

Good Scents ID

Not Available

References

Synthesis Reference

Abbott, Mitchel Theodore. The cell-free synthesis of 5-hydroxymethyluracil. (1963), 140 pp

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Faure H, Coudray C, Mousseau M, Ducros V, Douki T, Bianchini F, Cadet J, Favier A: 5-Hydroxymethyluracil excretion, plasma TBARS and plasma antioxidant vitamins in adriamycin-treated patients. Free Radic Biol Med. 1996;20(7):979-83. [PubMed:8743984 ]
Baker D, Liu P, Burdzy A, Sowers LC: Characterization of the substrate specificity of a human 5-hydroxymethyluracil glycosylase activity. Chem Res Toxicol. 2002 Jan;15(1):33-9. [PubMed:11800595 ]
Loft S, Poulsen HE: Estimation of oxidative DNA damage in man from urinary excretion of repair products. Acta Biochim Pol. 1998;45(1):133-44. [PubMed:9701506 ]
Ito T, van Kuilenburg AB, Bootsma AH, Haasnoot AJ, van Cruchten A, Wada Y, van Gennip AH: Rapid screening of high-risk patients for disorders of purine and pyrimidine metabolism using HPLC-electrospray tandem mass spectrometry of liquid urine or urine-soaked filter paper strips. Clin Chem. 2000 Apr;46(4):445-52. [PubMed:10759467 ]
Kow YW: Repair of deaminated bases in DNA. Free Radic Biol Med. 2002 Oct 1;33(7):886-93. [PubMed:12361800 ]
Kawasaki F, Beraldi D, Hardisty RE, McInroy GR, van Delft P, Balasubramanian S: Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania. Genome Biol. 2017 Jan 30;18(1):23. doi: 10.1186/s13059-017-1150-1. [PubMed:28137275 ]
Janouskova M, Vanikova Z, Nici F, Bohacova S, Vitovska D, Sanderova H, Hocek M, Krasny L: 5-(Hydroxymethyl)uracil and -cytosine as potential epigenetic marks enhancing or inhibiting transcription with bacterial RNA polymerase. Chem Commun (Camb). 2017 Dec 12;53(99):13253-13255. doi: 10.1039/c7cc08053k. [PubMed:29184924 ]

Showing metabocard for 5-Hydroxymethyluracil (HMDB0000469)

MOL for HMDB0000469 (5-Hydroxymethyluracil)

3D MOL for HMDB0000469 (5-Hydroxymethyluracil)

3D SDF for HMDB0000469 (5-Hydroxymethyluracil)

3D-SDF for HMDB0000469 (5-Hydroxymethyluracil)

PDB for HMDB0000469 (5-Hydroxymethyluracil)

3D PDB for HMDB0000469 (5-Hydroxymethyluracil)

SMILES for HMDB0000469 (5-Hydroxymethyluracil)

INCHI for HMDB0000469 (5-Hydroxymethyluracil)

Structure for HMDB0000469 (5-Hydroxymethyluracil)

3D Structure for HMDB0000469 (5-Hydroxymethyluracil)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra