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Showing metabocard for 5-Hydroxymethyluracil (HMDB0000469)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:52 UTC
HMDB IDHMDB0000469
Secondary Accession Numbers
  • HMDB00469
Metabolite Identification
Common Name5-Hydroxymethyluracil
Description5-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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000469 (5-Hydroxymethyluracil)

5-Hydroxymethyluracil.mol
  Mrv1652305271900002D          

 10 10  0  0  0  0            999 V2000
   -0.6187   -1.0717    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0313   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8563   -0.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    0.3572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2062    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    1.0717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2063   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4437   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8563   -1.0717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  1  8  1  0  0  0  0
  9 10  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000469 (5-Hydroxymethyluracil)

HMDB0000469
     RDKit          3D
5-Hydroxymethyluracil
 16 16  0  0  0  0  0  0  0  0999 V2000
   -3.3487    0.2489    0.2350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1348    0.1664    0.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4847   -1.0329   -0.1577 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1725   -1.1176   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5497    0.0309   -0.1732 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0607    0.0213   -0.2828 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5003   -0.7952    0.8090 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0664    1.2790    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6359    2.2882    0.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4595    1.2653    0.1579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0737   -1.9258   -0.1974 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3497   -2.0503   -0.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3102   -0.6497   -1.2012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5042    0.9299   -0.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7000   -0.8675    1.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8704    2.2092    0.3772 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  2  0
  8 10  1  0
 10  2  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
 10 16  1  0
M  END
Download

3D SDF for HMDB0000469 (5-Hydroxymethyluracil)

5-Hydroxymethyluracil.mol
  Mrv1652305271900002D          

 10 10  0  0  0  0            999 V2000
   -0.6187   -1.0717    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0313   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8563   -0.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    0.3572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2062    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    1.0717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2063   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4437   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8563   -1.0717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  1  8  1  0  0  0  0
  9 10  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000469

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C5H6N2O3

> <MOLECULAR_WEIGHT>
142.1127

> <EXACT_MASS>
142.037842068

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.341956480680967

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.31

> <JCHEM_LOGP>
-1.7405116673333332

> <ALOGPS_LOGS>
-1.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.309311051131726

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.683623447778928

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8444949646289412

> <JCHEM_POLAR_SURFACE_AREA>
78.43

> <JCHEM_REFRACTIVITY>
32.1011

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxymethyluracil

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000469 (5-Hydroxymethyluracil)

HMDB0000469
     RDKit          3D
5-Hydroxymethyluracil
 16 16  0  0  0  0  0  0  0  0999 V2000
   -3.3487    0.2489    0.2350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1348    0.1664    0.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4847   -1.0329   -0.1577 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1725   -1.1176   -0.2646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5497    0.0309   -0.1732 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0607    0.0213   -0.2828 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5003   -0.7952    0.8090 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0664    1.2790    0.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6359    2.2882    0.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4595    1.2653    0.1579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0737   -1.9258   -0.1974 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3497   -2.0503   -0.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3102   -0.6497   -1.2012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5042    0.9299   -0.4343 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7000   -0.8675    1.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8704    2.2092    0.3772 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  2  0
  8 10  1  0
 10  2  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
 10 16  1  0
M  END
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PDB for HMDB0000469 (5-Hydroxymethyluracil)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5-Hydroxymethyluracil.mol                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0      -1.155  -2.001   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.925  -0.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -3.465  -0.667   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      -1.155   0.667   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.385   0.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.155   2.001   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.155  -0.667   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.385  -2.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.695  -0.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.465  -2.001   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7    1                                                       
CONECT    9   10    7                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0000469 (5-Hydroxymethyluracil)

COMPND    HMDB0000469
HETATM    1  O1  UNL     1      -3.349   0.249   0.235  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.135   0.166   0.075  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.485  -1.033  -0.158  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.172  -1.118  -0.265  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.550   0.031  -0.173  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.061   0.021  -0.283  1.00  0.00           C  
HETATM    7  O2  UNL     1       2.500  -0.795   0.809  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.066   1.279   0.035  1.00  0.00           C  
HETATM    9  O3  UNL     1       0.636   2.288   0.084  1.00  0.00           O  
HETATM   10  N2  UNL     1      -1.460   1.265   0.158  1.00  0.00           N  
HETATM   11  H1  UNL     1      -2.074  -1.926  -0.197  1.00  0.00           H  
HETATM   12  H2  UNL     1       0.350  -2.050  -0.494  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.310  -0.650  -1.201  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.504   0.930  -0.434  1.00  0.00           H  
HETATM   15  H5  UNL     1       1.700  -0.867   1.432  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.870   2.209   0.377  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   11
CONECT    4    5    5   12
CONECT    5    6    8
CONECT    6    7   13   14
CONECT    7   15
CONECT    8    9    9   10
CONECT   10   16
END
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SMILES for HMDB0000469 (5-Hydroxymethyluracil)

OCC1=CNC(=O)NC1=O
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INCHI for HMDB0000469 (5-Hydroxymethyluracil)

InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-(Hydroxymethyl)-2,4(1H,3H)-pyrimidinedioneChEBI
5-(Hydroxymethyl)uracilChEBI
5-HYDROXYMETHYL uracilChEBI
5-(Hydroxymethyl)-1,3-dihydropyrimidine-2,4-dioneHMDB
a-HydroxythymineHMDB
alpha-HydroxythymineHMDB
HydroxymethyluracilHMDB
Chemical FormulaC5H6N2O3
Average Molecular Weight142.1127
Monoisotopic Molecular Weight142.037842068
IUPAC Name5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-hydroxymethyluracil
CAS Registry Number4433-40-3
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 KeyJDBGXEHEIRGOBU-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility44 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker124.49930932474
[M-H]-MetCCS_train_neg119.20830932474
[M-H]-Not Available121.9http://allccs.zhulab.cn/database/detail?ID=AllCCS00000325
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified0.12 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.0052 +/- 0.0026 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified88.0 +/- 8.0 uMAdult (>18 years old)Both
Solid tumors		 details
BloodDetected and Quantified42.0 +/- 21.0 uMAdult (>18 years old)Both
Solid tumors		 details
BloodDetected and Quantified15.0 +/- 2.0 uMAdult (>18 years old)Both
Solid tumors		 details
BloodDetected and Quantified63.0 +/- 5.0 uMAdult (>18 years old)Both
Solid tumors		 details
BloodDetected and Quantified33.0 +/- 4.0 uMAdult (>18 years old)Both
Solid tumors		 details
UrineDetected and Quantified0.0062 +/- 0.0023 umol/mmol creatinineAdult (>18 years old)BothSmoking details
Associated Disorders and Diseases
Disease References
Thymidine treatment
  1. 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
  1. 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 IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022061
KNApSAcK IDNot Available
Chemspider ID70544
KEGG Compound IDC03088
BioCyc IDCPD-254
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5456
PubChem Compound78168
PDB IDNot Available
ChEBI ID16964
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000168
Good Scents IDNot Available
References
Synthesis ReferenceAbbott, Mitchel Theodore. The cell-free synthesis of 5-hydroxymethyluracil. (1963), 140 pp
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. Kow YW: Repair of deaminated bases in DNA. Free Radic Biol Med. 2002 Oct 1;33(7):886-93. [PubMed:12361800 ]
  6. 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 ]
  7. 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 ]