4-amino-2-methyl-5-phosphomethylpyrimidine (YMDB00128)

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. In yeast, 4-amino-2-methyl-5-phosphomethylpyrimidine is involved in the metabolic pathway called the vitamin b1/thiamine metabolism pathway. Based on a literature review a small amount of articles have been published on 4-amino-2-methyl-5-phosphomethylpyrimidine.
Structure
Thumb
MOLSDFPDBSMILESInChI
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-methylpyrimidine → 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP
Adenosine triphosphate + 4-amino-2-methyl-5-phosphomethylpyrimidine → ADP + 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-methylpyrimidine → 4-amino-2-methyl-5-phosphomethylpyrimidine + hydron + ADP
4-amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate → 4-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 GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0490000000-d0df918acbe4ba0a1686JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00e9-8900000000-4224a9cd25055b1596c1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0560-9200000000-d4f98d693c874da458adJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9010000000-28b8f8a4523c0b4ca1a8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
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 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
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 IDHMDB0243613
Pubchem Compound ID216
Kegg IDC04556
ChemSpider ID211
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI21
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.
Protein Details
2. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
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.
Protein Details
3. Thiamine biosynthesis protein THI22
General function:
Coenzyme transport and metabolism
Specific function:
Essential for thiamine biosynthesis
Gene Name:
THI22
Uniprot ID:
Q06490
Molecular weight:
63306.39844
Reactions