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 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
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 IDNot Available
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.