Survey with prize
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00118
Name4-amino-5-hydroxymethyl-2-methylpyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description4-Amino-5-hydroxymethyl-2-methylpyrimidine, also known as toxopyrimidine or pyramine, belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.). In yeast, 4-amino-5-hydroxymethyl-2-methylpyrimidine is involved in the metabolic pathway called the vitamin b1/thiamine metabolism pathway. Based on a literature review a significant number of articles have been published on 4-Amino-5-hydroxymethyl-2-methylpyrimidine.
Structure
Thumb
Synonyms
  • (4-amino-2-methyl-5-pyrimidinyl)methanol
  • 4-amino-2-methyl-5-hydroxymethylpyrimidine
  • 4-Amino-2-methyl-5-pyrimidinemethanol
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine
  • 5-Pyrimidinemethanol, 4-amino-2-methyl-
  • Atoxopyrimidine
  • OMPM
  • Pyramin (VAN)
  • Pyramine
  • Pyramine (thiamine metabolite)
  • Pyramine (VAN)
  • Pyrazan
  • Toxopyrimidine
  • TXP
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine
  • Pyramin
  • HMP
  • HMP CPD
CAS number73-67-6
WeightAverage: 139.1552
Monoisotopic: 139.074561925
InChI KeyVUTBELPREDJDDH-UHFFFAOYSA-N
InChIInChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
IUPAC Name(4-amino-2-methylpyrimidin-5-yl)methanol
Traditional IUPAC Nametoxopyrimidine
Chemical FormulaC6H9N3O
SMILESCC1=NC=C(CO)C(N)=N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydropyrimidines
Alternative Parents
Substituents
  • Imidolactam
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point198 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility12 g/LALOGPS
logP-0.26ALOGPS
logP-0.36ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)14.41ChemAxon
pKa (Strongest Basic)6.17ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.18 m³·mol⁻¹ChemAxon
Polarizability14.2 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Vitamin B1/Thiamine metabolismPW002486 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Thiamine metabolismec00730 Map00730
SMPDB Reactions
Adenosine triphosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine4-amino-2-methyl-5-phosphomethylpyrimidine + ADP
4-amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate ADP + hydron + 4-amino-2-methyl-5-phosphomethylpyrimidine
pyrithiamine + water + oxidized electron acceptor → 4-amino-5-hydroxymethyl-2-methylpyrimidine + 2-(2-methylpyridin-3-yl)ethanol + reduced electron acceptor
KEGG Reactions
5-Aminoimidazole ribonucleotide + hydronGlycolaldehyde + phosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine
Adenosine triphosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine4-amino-2-methyl-5-phosphomethylpyrimidine + hydron + ADP
Thiamine + waterhydron + 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-Hydroxyethyl)-4-methylthiazole
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0abi-1900000000-e3106b1f3a699dcbb5cfJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-006x-0900000000-1464721132642f06c763JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-1900000000-ffcb98d194c46375afedJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-007k-9200000000-146c29035e7732b4a386JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-a6fee6edf0aa915e501aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-4900000000-7fb22624813fc7a88208JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-fd0e2a1b16eb26493e89JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00dl-0900000000-bcee92b22282400d9aa9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00e9-7900000000-c3b2ba29d4a3384fbf9fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00lu-9000000000-cecde0be355431a2920bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-cfc1d884f8ea3db6b6a6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006x-8900000000-bb08081d11c0ce993537JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-014l-9000000000-f27a78acaec6ce875983JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Kawasaki, Y., Onozuka, M., Mizote, T., Nosaka, K. (2005). "Biosynthesis of hydroxymethylpyrimidine pyrophosphate in Saccharomyces cerevisiae." Curr Genet 47:156-162.15614489
  • Onozuka, M., Konno, H., Kawasaki, Y., Akaji, K., Nosaka, K. (2008). "Involvement of thiaminase II encoded by the THI20 gene in thiamin salvage of Saccharomyces cerevisiae." FEMS Yeast Res 8:266-275.18028398
  • Kawasaki, Y., Nosaka, K., Kaneko, Y., Nishimura, H., Iwashima, A. (1990). "Regulation of thiamine biosynthesis in Saccharomyces cerevisiae." J Bacteriol 172:6145-6147.2170344
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16892
HMDB IDHMDB0247327
Pubchem Compound ID777
Kegg IDC01279
ChemSpider ID756
FOODB IDFDB030912
Wikipedia ID4-Amino-5-hydroxymethyl-2-methylpyrimidine
BioCyc IDNot Available

Enzymes

General function:
Involved in phosphomethylpyrimidine kinase activity
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and also probaby that of HMP to HMP- P
Gene Name:
THI21
Uniprot ID:
Q08975
Molecular weight:
61333.69922
Reactions
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine → ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine.
ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
General function:
Involved in phosphomethylpyrimidine kinase activity
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and also probaby that of HMP to HMP- P
Gene Name:
THI20
Uniprot ID:
Q08224
Molecular weight:
61268.89844
Reactions
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine → ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine.
ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
thiamine + H2O → 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole.
General function:
Coenzyme transport and metabolism
Specific function:
Essential for thiamine biosynthesis
Gene Name:
THI22
Uniprot ID:
Q06490
Molecular weight:
63306.39844
Reactions