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Identification
YMDB IDYMDB00128
Name4-amino-2-methyl-5-phosphomethylpyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description4-amino-2-methyl-5-phosphomethylpyrimidine, also known as HMP-p or (4-amino-2-methylpyrimidin-5-yl)methyl phosphate, belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. 4-amino-2-methyl-5-phosphomethylpyrimidine is a very strong basic compound (based on its pKa). 4-amino-2-methyl-5-phosphomethylpyrimidine exists in both E. coli (prokaryote) and yeast (eukaryote). Within yeast, 4-amino-2-methyl-5-phosphomethylpyrimidine participates in a number of enzymatic reactions. In particular, 4-amino-2-methyl-5-phosphomethylpyrimidine can be converted into 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate; which is catalyzed by the enzyme hydroxymethylpyrimidine/phosphomethylpyrimidine kinase. In addition, 4-amino-2-methyl-5-phosphomethylpyrimidine can be biosynthesized from 4-amino-5-hydroxymethyl-2-methylpyrimidine through its interaction with the enzyme hydroxymethylpyrimidine/phosphomethylpyrimidine kinase. In yeast, 4-amino-2-methyl-5-phosphomethylpyrimidine is involved in the metabolic pathway called the vitamin b1/thiamine metabolism pathway.
Structure
Thumb
Synonyms
  • 4-Amino-2-methyl-5-phosphomethylpyrimidine
  • 4-Amino-5-phosphomethyl-2-methylpyrimidine
  • 4-Amino-2-methyl-5-hydroxymethylpyrimidine phosphate
  • 4-Amino-2-methyl-5-phosphonooxymethylpyrimidine
  • HMP-p
  • (4-Amino-2-methylpyrimidin-5-yl)methyl phosphate
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate
  • 4-Amino-2-methyl-5-hydroxymethylpyrimidine phosphoric acid
  • (4-Amino-2-methylpyrimidin-5-yl)methyl phosphoric acid
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphoric acid
CAS numberNot Available
WeightAverage: 219.1351
Monoisotopic: 219.040892335
InChI KeyPKYFHKIYHBRTPI-UHFFFAOYSA-N
InChIInChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)
IUPAC Name[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphonic acid
Traditional IUPAC Name(4-imino-2-methyl-3H-pyrimidin-5-yl)methoxyphosphonic acid
Chemical FormulaC6H10N3O4P
SMILESCC1=NC=C(COP(O)(O)=O)C(N)=N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. 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 ParentAminopyrimidines and derivatives
Alternative Parents
Substituents
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Imidolactam
  • Heteroaromatic compound
  • Azacycle
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.76 g/LALOGPS
logP-1.1ALOGPS
logP-1.8ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)1.62ChemAxon
pKa (Strongest Basic)7.59ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity58.83 m³·mol⁻¹ChemAxon
Polarizability18.83 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
Adenosine triphosphate + 4-amino-2-methyl-5-phosphomethylpyrimidineADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
4-amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate ADP + hydron + 4-amino-2-methyl-5-phosphomethylpyrimidine
KEGG Reactions
Adenosine triphosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine4-amino-2-methyl-5-phosphomethylpyrimidine + hydron + ADP
4-amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate4-amino-2-methyl-5-diphosphomethylpyrimidine + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-9620000000-67208cb5c399d7eb0927JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-1690000000-b4b286e97e3c3859ded5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-2900000000-ef20fcb4606f47d76648JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00ea-9400000000-23f2dc587b8ee21085afJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-016s-9080000000-bb863e533b4baa6368fdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-f35dbb3f524d9e7e08e0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-04a487a0ef46589c29a0JSpectraViewer
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., Nosaka, K., Kaneko, Y., Nishimura, H., Iwashima, A. (1990). "Regulation of thiamine biosynthesis in Saccharomyces cerevisiae." J Bacteriol 172:6145-6147.2170344
  • Llorente, B., Fairhead, C., Dujon, B. (1999). "Genetic redundancy and gene fusion in the genome of the Baker's yeast Saccharomyces cerevisiae: functional characterization of a three-member gene family involved in the thiamine biosynthetic pathway." Mol Microbiol 32:1140-1152.10383756
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18032
HMDB IDNot Available
Pubchem Compound ID216
Kegg IDC04556
ChemSpider ID211
FOODB IDNot Available
Wikipedia IDNot Available
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