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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 4-amino-2-methyl-5-pyrimidinemethanol, 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.). 4-Amino-5-hydroxymethyl-2-methylpyrimidine is a very strong basic compound (based on its pKa). 4-Amino-5-hydroxymethyl-2-methylpyrimidine exists in both E. coli (prokaryote) and yeast (eukaryote). Within yeast, 4-amino-5-hydroxymethyl-2-methylpyrimidine participates in a number of enzymatic reactions. In particular, 4-amino-5-hydroxymethyl-2-methylpyrimidine can be converted into 4-amino-2-methyl-5-phosphomethylpyrimidine through the action of the enzyme hydroxymethylpyrimidine/phosphomethylpyrimidine kinase. In addition, 4-amino-5-hydroxymethyl-2-methylpyrimidine and 2-(2-methylpyridin-3-yl)ethanol can be biosynthesized from pyrithiamine; which is mediated by the enzyme thiaminase 2. In yeast, 4-amino-5-hydroxymethyl-2-methylpyrimidine is involved in the metabolic pathway called the vitamin b1/thiamine metabolism pathway.
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 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 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
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 IDNot Available
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