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Showing metabocard for 5-Hydroxymethyl-4-methyluracil (HMDB0000544)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:56 UTC
HMDB IDHMDB0000544
Secondary Accession Numbers
  • HMDB00544
Metabolite Identification
Common Name5-Hydroxymethyl-4-methyluracil
Description5-Hydroxymethyl-4-methyluracil, also known as pentoxyl or 4-methyl-5-hydroxymethyluracil, 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-Hydroxymethyl-4-methyluracil has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 5-hydroxymethyl-4-methyluracil a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 5-Hydroxymethyl-4-methyluracil.
Structure
Data?1676999696
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

5-Hydroxymethyl-4-methyluracil.mol
  Mrv1652305271900002D          

 11 11  0  0  0  0            999 V2000
    1.0313    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2063    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8563    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4437    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8563   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  1  7  2  0  0  0  0
  3  8  2  0  0  0  0
  5  9  1  0  0  0  0
 10 11  1  0  0  0  0
  4 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

HMDB0000544
     RDKit          3D
5-Hydroxymethyl-4-methyluracil
 19 19  0  0  0  0  0  0  0  0999 V2000
    0.0058    2.1306    0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4918    0.7423    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8153    0.4434   -0.0879 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2406   -0.8367   -0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4685   -1.0937   -0.1946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3404   -1.8312   -0.0436 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0179   -1.5963    0.0468 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8303   -2.5091    0.1100 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4224   -0.2858    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8649    0.0537    0.1688 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5698   -1.1465    0.2236 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7418    2.3143    0.8365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8455    2.8303    0.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4766    2.4446   -0.9166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4781    1.2490   -0.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6685   -2.8199   -0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2299    0.6116   -0.7149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0912    0.5929    1.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1340   -1.2934   -0.5654 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9  2  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
 10 17  1  0
 10 18  1  0
 11 19  1  0
M  END
Download

3D SDF for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

5-Hydroxymethyl-4-methyluracil.mol
  Mrv1652305271900002D          

 11 11  0  0  0  0            999 V2000
    1.0313    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2063    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8563    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6188    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4437    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8563   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  1  7  2  0  0  0  0
  3  8  2  0  0  0  0
  5  9  1  0  0  0  0
 10 11  1  0  0  0  0
  4 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000544

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(CO)C(=O)NC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8N2O3/c1-3-4(2-9)5(10)8-6(11)7-3/h9H,2H2,1H3,(H2,7,8,10,11)

> <INCHI_KEY>
XBAVGYMDOXCWQU-UHFFFAOYSA-N

> <FORMULA>
C6H8N2O3

> <MOLECULAR_WEIGHT>
156.1393

> <EXACT_MASS>
156.053492132

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.30985910387299

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(hydroxymethyl)-6-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.95

> <JCHEM_LOGP>
-1.5384389573333332

> <ALOGPS_LOGS>
-1.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.45337652276045

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.96507194565207

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8488067546609095

> <JCHEM_POLAR_SURFACE_AREA>
78.42999999999999

> <JCHEM_REFRACTIVITY>
37.9202

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.50e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxymethyl-6-methyluracil

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

HMDB0000544
     RDKit          3D
5-Hydroxymethyl-4-methyluracil
 19 19  0  0  0  0  0  0  0  0999 V2000
    0.0058    2.1306    0.0297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4918    0.7423    0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8153    0.4434   -0.0879 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2406   -0.8367   -0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4685   -1.0937   -0.1946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3404   -1.8312   -0.0436 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0179   -1.5963    0.0468 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8303   -2.5091    0.1100 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4224   -0.2858    0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8649    0.0537    0.1688 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5698   -1.1465    0.2236 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7418    2.3143    0.8365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8455    2.8303    0.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4766    2.4446   -0.9166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4781    1.2490   -0.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6685   -2.8199   -0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2299    0.6116   -0.7149 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0912    0.5929    1.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1340   -1.2934   -0.5654 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
  9  2  2  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
 10 17  1  0
 10 18  1  0
 11 19  1  0
M  END
Download

PDB for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5-Hydroxymethyl-4-methyluracil.mol                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.925   0.000   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.155  -1.334   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.385  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.155   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.385   1.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.155   1.334   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       3.465   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.155  -2.667   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.155   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.695   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.465  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    1                                                       
CONECT    7    1                                                            
CONECT    8    3                                                            
CONECT    9    5                                                            
CONECT   10   11    4                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

COMPND    HMDB0000544
HETATM    1  C1  UNL     1       0.006   2.131   0.030  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.492   0.742   0.002  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.815   0.443  -0.088  1.00  0.00           N  
HETATM    4  C3  UNL     1      -2.241  -0.837  -0.111  1.00  0.00           C  
HETATM    5  O1  UNL     1      -3.469  -1.094  -0.195  1.00  0.00           O  
HETATM    6  N2  UNL     1      -1.340  -1.831  -0.044  1.00  0.00           N  
HETATM    7  C4  UNL     1      -0.018  -1.596   0.047  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.830  -2.509   0.110  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.422  -0.286   0.071  1.00  0.00           C  
HETATM   10  C6  UNL     1       1.865   0.054   0.169  1.00  0.00           C  
HETATM   11  O3  UNL     1       2.570  -1.146   0.224  1.00  0.00           O  
HETATM   12  H1  UNL     1       0.742   2.314   0.837  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.846   2.830   0.229  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.477   2.445  -0.917  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.478   1.249  -0.138  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.669  -2.820  -0.061  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.230   0.612  -0.715  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.091   0.593   1.116  1.00  0.00           H  
HETATM   19  H8  UNL     1       3.134  -1.293  -0.565  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    9    9
CONECT    3    4   15
CONECT    4    5    5    6
CONECT    6    7   16
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   17   18
CONECT   11   19
END
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SMILES for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

CC1=C(CO)C(=O)NC(=O)N1
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INCHI for HMDB0000544 (5-Hydroxymethyl-4-methyluracil)

InChI=1S/C6H8N2O3/c1-3-4(2-9)5(10)8-6(11)7-3/h9H,2H2,1H3,(H2,7,8,10,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
PentoxylHMDB
4-Methyl-5-hydroxymethyluracilHMDB
5-Hydroxymethyl-6-methyluracilHMDB
PentoxilHMDB
Chemical FormulaC6H8N2O3
Average Molecular Weight156.1393
Monoisotopic Molecular Weight156.053492132
IUPAC Name5-(hydroxymethyl)-6-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name5-hydroxymethyl-6-methyluracil
CAS Registry Number147-61-5
SMILES
CC1=C(CO)C(=O)NC(=O)N1
InChI Identifier
InChI=1S/C6H8N2O3/c1-3-4(2-9)5(10)8-6(11)7-3/h9H,2H2,1H3,(H2,7,8,10,11)
InChI KeyXBAVGYMDOXCWQU-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 DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility9.5 g/LALOGPS
logP-0.95ALOGPS
logP-1.5ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)8.97ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.92 m³·mol⁻¹ChemAxon
Polarizability14.31 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+133.14631661259
DarkChem[M-H]-130.71331661259
AllCCS[M+H]+132.83232859911
AllCCS[M-H]-129.95932859911
DeepCCS[M+H]+136.06830932474
DeepCCS[M-H]-132.56330932474
DeepCCS[M-2H]-170.03430932474
DeepCCS[M+Na]+145.21430932474
AllCCS[M+H]+132.832859911
AllCCS[M+H-H2O]+128.432859911
AllCCS[M+NH4]+137.032859911
AllCCS[M+Na]+138.232859911
AllCCS[M-H]-130.032859911
AllCCS[M+Na-2H]-131.432859911
AllCCS[M+HCOO]-133.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
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, 2022.2.33 minutes32390414
Predicted by Siyang on May 30, 20229.0303 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.88 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid551.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid309.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid66.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid178.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid44.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid254.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid256.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)492.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid591.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid96.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid797.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid184.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid191.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate573.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA297.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water309.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Hydroxymethyl-4-methyluracilCC1=C(CO)C(=O)NC(=O)N12671.9Standard polar33892256
5-Hydroxymethyl-4-methyluracilCC1=C(CO)C(=O)NC(=O)N11726.1Standard non polar33892256
5-Hydroxymethyl-4-methyluracilCC1=C(CO)C(=O)NC(=O)N12024.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Hydroxymethyl-4-methyluracil,1TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)[NH]C(=O)[NH]11578.7Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,1TMS,isomer #2CC1=C(CO)C(=O)N([Si](C)(C)C)C(=O)[NH]11610.2Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,1TMS,isomer #3CC1=C(CO)C(=O)[NH]C(=O)N1[Si](C)(C)C1630.7Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C1696.2Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C1898.6Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C2057.9Standard polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #2CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]11692.7Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #2CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]11837.5Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #2CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)[NH]12041.8Standard polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1693.3Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1905.2Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2028.4Standard polar33892256
5-Hydroxymethyl-4-methyluracil,3TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1908.6Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,3TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1930.2Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,3TMS,isomer #1CC1=C(CO[Si](C)(C)C)C(=O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C1892.9Standard polar33892256
5-Hydroxymethyl-4-methyluracil,1TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)[NH]C(=O)[NH]11837.3Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,1TBDMS,isomer #2CC1=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]11868.0Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,1TBDMS,isomer #3CC1=C(CO)C(=O)[NH]C(=O)N1[Si](C)(C)C(C)(C)C1886.1Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C(C)(C)C2145.0Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C(C)(C)C2341.3Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)[NH]C(=O)N1[Si](C)(C)C(C)(C)C2239.0Standard polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #2CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12108.5Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #2CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12264.1Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #2CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)[NH]12224.7Standard polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2193.5Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2331.3Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,2TBDMS,isomer #3CC1=C(CO)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2205.7Standard polar33892256
5-Hydroxymethyl-4-methyluracil,3TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2436.3Semi standard non polar33892256
5-Hydroxymethyl-4-methyluracil,3TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2553.4Standard non polar33892256
5-Hydroxymethyl-4-methyluracil,3TBDMS,isomer #1CC1=C(CO[Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2271.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (Non-derivatized) - 70eV, Positivesplash10-0570-2900000000-6d3123b130d7ec19e8082017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (1 TMS) - 70eV, Positivesplash10-00di-8950000000-403e445cdfceda8a33dc2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Hydroxymethyl-4-methyluracil GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-000i-1900000000-98840e3cfa5ad76a2bfd2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-052e-9000000000-15bce94c97d641aed0f02012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0006-9000000000-211a07c5fca58f18f1262012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 10V, Positive-QTOFsplash10-0a4r-0900000000-6787b038f231e886bb7a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 20V, Positive-QTOFsplash10-000i-2900000000-321ae27f5314a308c9c12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 40V, Positive-QTOFsplash10-03di-6900000000-99ca165b30e7d4e910b02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 10V, Negative-QTOFsplash10-0a6u-2900000000-3a8e88ff3873e9d0667b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 20V, Negative-QTOFsplash10-0036-9400000000-b99bae4706524c3384432017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 40V, Negative-QTOFsplash10-0006-9000000000-0457a74a96fdfae0fcad2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 10V, Negative-QTOFsplash10-0a4r-0900000000-b08c62b8b31b36149b5b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 20V, Negative-QTOFsplash10-0006-9700000000-3d2a8012e24000e8a17f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 40V, Negative-QTOFsplash10-0006-9000000000-ebc6a7bfd34c1e35ad902021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 10V, Positive-QTOFsplash10-0a4i-0900000000-3d165e67798530b1a5ec2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 20V, Positive-QTOFsplash10-0a4r-2900000000-f01651a8023416380c212021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Hydroxymethyl-4-methyluracil 40V, Positive-QTOFsplash10-0udi-9000000000-6de7b611c9a2831c4cac2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)2012-12-05Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022107
KNApSAcK IDNot Available
Chemspider ID8635
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5529
PubChem Compound8983
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceCannon-Carlson S V; Gokhale H; Teebor G W Purification and characterization of 5-hydroxymethyluracil-DNA glycosylase from calf thymus. Its possible role in the maintenance of methylated cytosine residues. The Journal of biological chemistry (1989), 264(22), 13306-12.
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available