Record Information
Version2.0
Creation Date2012-05-31 14:26:35 -0600
Update Date2015-10-15 16:14:23 -0600
Secondary Accession Numbers
  • ECMDB20084
Identification
Name:4-Amino-2-methyl-5-phosphomethylpyrimidine
Description4-amino-2-methyl-5-phosphomethylpyrimidine 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. Tomato LeTHIC is an Fe-requiring HMP-P synthase involved in thiamine synthesis and regulated by multiple factors. (PMID 21511719) Although each isoform independently can synthesize HMP pyrophosphate (HMP-PP) from HMP, there is a marked difference in efficiency between the two proteins. (PMID 15614489)
Structure
Thumb
Synonyms:
  • (4-amino-2-methylpyrimidin-5-yl)methyl dihydrogen phosphate
  • (4-amino-2-Methylpyrimidin-5-yl)methyl dihydrogen phosphoric acid
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine-P
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine-phosphate
  • 4-amino-5-Hydroxymethyl-2-methylpyrimidine-phosphoric acid
  • 4-Amino-5-phosphomethyl-2-methylpyrimidine
  • HMePyrP
  • HMP-P
Chemical Formula:C6H8N3O4P
Weight:Average: 217.122
Monoisotopic: 217.026339907
InChI Key:PKYFHKIYHBRTPI-UHFFFAOYSA-L
InChI:InChI=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)/p-2
CAS number:Not Available
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
SMILES:CC1=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
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Reactions:
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + Water > 4-Amino-2-methyl-5-phosphomethylpyrimidine + Hydrogen ion + Phosphate
4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <> 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
4-Amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate > 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + ADP
5-Aminoimidazole ribonucleotide + Water + NAD > 4-Amino-2-methyl-5-phosphomethylpyrimidine +2 Formic acid +3 Hydrogen ion + NADH
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-2-methyl-5-phosphomethylpyrimidine <> ADP + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine <> Hydrogen ion + ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine
5-Aminoimidazole ribonucleotide + S-Adenosylmethionine 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + carbon monoxide + Hydrogen ion
5-Aminoimidazole ribonucleotide + S-adenosyl-L-methionine > 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
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:
  • 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis PWY-6890
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-9620000000-67208cb5c399d7eb0927View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-1690000000-b4b286e97e3c3859ded5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-2900000000-ef20fcb4606f47d76648View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00ea-9400000000-23f2dc587b8ee21085afView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-016s-9080000000-bb863e533b4baa6368fdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-f35dbb3f524d9e7e08e0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-04a487a0ef46589c29a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0490000000-d0df918acbe4ba0a1686View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00e9-8900000000-4224a9cd25055b1596c1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0560-9200000000-d4f98d693c874da458adView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9010000000-28b8f8a4523c0b4ca1a8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
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 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
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
  • Kawasaki, Y., Onozuka, M., Mizote, T., Nosaka, K. (2005). "Biosynthesis of hydroxymethylpyrimidine pyrophosphate in Saccharomyces cerevisiae." Curr Genet 47:156-162. Pubmed: 15614489
  • 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
  • Zhao, W., Cheng, X., Huang, Z., Fan, H., Wu, H., Ling, H. Q. (2011). "Tomato LeTHIC is an Fe-requiring HMP-P synthase involved in thiamine synthesis and regulated by multiple factors." Plant Cell Physiol 52:967-982. Pubmed: 21511719
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18032
HMDB IDHMDB0243613
Pubchem Compound ID216
Kegg IDC04556
ChemSpider ID211
Wikipedia IDNot Available
BioCyc IDAMINO-HYDROXYMETHYL-METHYL-PYR-P
EcoCyc IDAMINO-HYDROXYMETHYL-METHYL-PYR-P
Ligand ExpoMP5

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Catalyzes the hydrolysis of 4-amino-2-methyl-5- hydroxymethylpyrimidine pyrophosphate (HMP-PP) to 4-amino-2- methyl-5-hydroxymethylpyrimidine phosphate (HMP-P), and hydrolysis of thiamine pyrophosphate (TPP) to thiamine monophosphate (TMP). Can hydrolyze other substrates such as MeO-HMP-PP, CF(3)-HMP-PP and MeO-TPP. Is also a non-specific nucleoside tri- and diphosphatase that releases inorganic orthophosphate
Gene Name:
nudJ
Uniprot ID:
P0AEI6
Molecular weight:
17433
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 catalytic activity
Specific function:
Catalyzes the hydrolysis of 4-amino-2-methyl-5- hydroxymethylpyrimidine pyrophosphate (HMP-PP) to 4-amino-2- methyl-5-hydroxymethylpyrimidine phosphate (HMP-P). Can also hydrolyze other substrates such as MeO-HMP-PP and CF(3)-HMP-PP
Gene Name:
cof
Uniprot ID:
P46891
Molecular weight:
30371
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.