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Showing NP-Card for 5-Hydroxymethyluracil (NP0000463)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-09 22:33:05 UTC
NP-MRD IDNP0000463
Secondary Accession NumbersNone
Natural Product 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 NP0000463 (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 NP0000463 (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 NP0000463 (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>
NP0000463

> <DATABASE_NAME>
NP-MRD

> <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 NP0000463 (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

PDB for NP0000463 (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 NP0000463 (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 NP0000463 (5-Hydroxymethyluracil)

OCC1=CNC(=O)NC1=O
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INCHI for NP0000463 (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 JSmol
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 Mass142.1127 Da
Monoisotopic Mass142.03784 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility44 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14 g/LALOGPS
logP-1.3ALOGPS
logP-1.7ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)8.68ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.1 m³·mol⁻¹ChemAxon
Polarizability12.34 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000469
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]