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 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
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 IDNot Available
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.