Record Information
Version2.0
Creation Date2012-05-31 14:26:41 -0600
Update Date2015-06-03 17:19:17 -0600
Secondary Accession Numbers
  • ECMDB20086
Identification
Name:4-Amino-5-hydroxymethyl-2-methylpyrimidine
Description4-amino-5-hydroxymethyl-2-methylpyrimidine is a member of the chemical class known as Pyrimidines and Pyrimidine Derivatives. These are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms. The conversion of 5-aminoimidazole ribonucleotide (AIR) into 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) is a fascinating reaction on the thiamin biosynthetic pathway in bacteria and is probably the most complex unresolved rearrangement in primary metabolism. (PMID 15326535)
Structure
Thumb
Synonyms:
  • (4-Amino-2-methyl-5-pyrimidinyl)methanol
  • (4-amino-2-methylpyrimidin-5-yl)methanol
  • 2-M-4-A-5-Hmp
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine
  • 4-Amino-2-methyl-5-hydroxymethylpyrimidine
  • 4-Amino-2-methyl-5-pyrimidinemethanol
  • 4-amino-5-hydroxymethyl-2-methylpyrimidine
  • 5-Pyrimidinemethanol, 4-amino-2-methyl- (8CI)(9CI)
  • 6-Amino-5-hydroxymethyl-2-methylpyrimidine
  • Atoxopyrimidine
  • HMePyr
  • HMH
  • HMP
  • Hydroxymethylpyrimidine
  • Nchembio.121-comp11
  • NChemBio.2007.13-comp6
  • OMPM
  • Oxymethylpyrimidine
  • Pyramin
  • Pyramin (van)
  • Pyramine
  • Pyramine (thiamine metabolite)
  • Pyramine (van)
  • Pyrazan
  • Toxopyrimidine
  • TXP
Chemical Formula:C6H9N3O
Weight:Average: 139.1552
Monoisotopic: 139.074561925
InChI Key:VUTBELPREDJDDH-UHFFFAOYSA-N
InChI:InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
CAS number:73-67-6
IUPAC Name:(4-amino-2-methylpyrimidin-5-yl)methanol
Traditional IUPAC Name:toxopyrimidine
SMILES:CC1=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
State:Solid
Charge:0
Melting point:198 °C
Experimental Properties:
PropertyValueSource
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
Reactions:
4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <> 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine <> ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine
4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <> 5-Aminoimidazole ribonucleotide + 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine <> Hydrogen ion + ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine > ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine
4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <>4 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion +4 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <>5 5-Aminoimidazole ribonucleotide +4 4-Amino-2-methyl-5-phosphomethylpyrimidine +5 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <>4 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion +4 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <>5 5-Aminoimidazole ribonucleotide +4 4-Amino-2-methyl-5-phosphomethylpyrimidine +5 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0abi-1900000000-e3106b1f3a699dcbb5cfView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-006x-0900000000-1464721132642f06c763View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-1900000000-ffcb98d194c46375afedView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-007k-9200000000-146c29035e7732b4a386View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-a6fee6edf0aa915e501aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-4900000000-7fb22624813fc7a88208View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-fd0e2a1b16eb26493e89View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00dl-0900000000-bcee92b22282400d9aa9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00e9-7900000000-c3b2ba29d4a3384fbf9fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00lu-9000000000-cecde0be355431a2920bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0900000000-cfc1d884f8ea3db6b6a6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006x-8900000000-bb08081d11c0ce993537View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-014l-9000000000-f27a78acaec6ce875983View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Lawhorn, B. G., Mehl, R. A., Begley, T. P. (2004). "Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction." Org Biomol Chem 2:2538-2546. Pubmed: 15326535
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16892
HMDB IDHMDB0247327
Pubchem Compound ID777
Kegg IDC01279
ChemSpider ID756
Wikipedia ID4-Amino-5-hydroxymethyl-2-methylpyrimidine
BioCyc IDHMP
EcoCyc IDHMP
Ligand ExpoHMH

Enzymes

General function:
Involved in pyridoxal kinase activity
Specific function:
Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates
Gene Name:
pdxK
Uniprot ID:
P40191
Molecular weight:
30847
Reactions
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
General function:
Involved in phosphomethylpyrimidine kinase activity
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P. Shows no activity with pyridoxal, pyridoxamine or pyridoxine
Gene Name:
thiD
Uniprot ID:
P76422
Molecular weight:
28633
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 thiamine biosynthetic process
Specific function:
Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
Gene Name:
thiC
Uniprot ID:
P30136
Molecular weight:
70850
Reactions
5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO.