2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (ECMDB20046) (M2MDB000895)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (4)XML
Proteins (906)
Record Information
Version2.0
Creation Date2012-05-31 14:24:37 -0600
Update Date2015-09-18 09:17:42 -0600
Secondary Accession Numbers
  • ECMDB20046
Identification
Name:2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
Description2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. HMP-PP is involved in thiamin biosynthesis. Two redundant genes, THI20 and THI21, of Saccharomyces cerevisiae encode a 2-methyl-4-amino-5-hydroxymethylpyrimidine monophosphate (HMP-P) kinase required for thiamin biosynthesis. 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
MOLSDFPDBSMILESInChI
Synonyms:
  • (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
  • (4-amino-2-Methylpyrimidin-5-yl)methyl diphosphoric acid
  • 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphoric acid
  • 4-Amino-2-methyl-5-diphosphomethylpyrimidine
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine-PP
  • 4A5HMe2MePyrPP
  • HMP-PP
Chemical Formula:C6H8N3O7P2
Weight:Average: 296.093
Monoisotopic: 295.985394345
InChI Key:AGQJQCFEPUVXNK-UHFFFAOYSA-K
InChI:InChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)/p-3
CAS number:Not Available
IUPAC Name:{[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphonato]oxy}phosphonate
Traditional IUPAC Name:[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphonato]oxyphosphonate
SMILES:CC1=NC=C(COP([O-])(=O)OP([O-])([O-])=O)C(=N)N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • Amine
  • Primary amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organic anion
  • 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 Solubility12.2 g/LALOGPS
logP-0.34ALOGPS
logP-2.8ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)12.19ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area170.02 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity66.33 m³·mol⁻¹ChemAxon
Polarizability22.61 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-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate > 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + ADP
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-Methyl-5-(2-phosphoethyl)-thiazole + Hydrogen ion <> Pyrophosphate + Thiamine monophosphate
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-Methyl-5-(2-phosphoethyl)-thiazole <> Pyrophosphate + Thiamine monophosphate
Adenosine triphosphate + 4-Amino-2-methyl-5-phosphomethylpyrimidine <> ADP + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
2-[(2<i>R</i>,5<i>Z</i>)-(2-carboxy-4-methylthiazol-5(2<i>H</i>)-ylidene]ethyl phosphate + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + Hydrogen ion > Thiamine monophosphate + Carbon dioxide + Pyrophosphate
Hydrogen ion + 4-Methyl-5-(2-phosphoethyl)-thiazole + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate > Thiamine monophosphate + Pyrophosphate
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-Methyl-5-(2-phosphoethyl)-thiazole > Pyrophosphate + Thiamine monophosphate
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + 2 Hydrogen ion + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate > Thiamine monophosphate + Carbon dioxide + diphosphate + Thiamine monophosphate + Pyrophosphate
Pyridoxal 5'-phosphate > 4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
4-amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate > ADP + 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + Hydrogen ion > Carbon dioxide + Pyrophosphate + Thiamine monophosphate
2 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4 4-Methyl-5-(2-phosphoethyl)-thiazole + Hydrogen ion <> Pyrophosphate + Thiamine monophosphate
SMPDB Pathways:
Thiamin diphosphate biosynthesisPW002028 ThumbThumb?image type=greyscaleThumb?image type=simple
Vitamin B1/ThiaminePW000892 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis PWY-6890
  • thiamin diphosphate biosynthesis I (E. coli) PWY-6894
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16629
HMDB IDHMDB0304168
Pubchem Compound ID217
Kegg IDC04752
ChemSpider ID212
Wikipedia IDNot Available
BioCyc IDAMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP
EcoCyc IDAMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP

Enzymes

Protein Details
1. Phosphatase nudJ
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
Protein Details
2. Thiamine-phosphate pyrophosphorylase
General function:
Involved in catalytic activity
Specific function:
Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP)
Gene Name:
thiE
Uniprot ID:
P30137
Molecular weight:
23015
Reactions
2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)thiazole = diphosphate + thiamine phosphate.
Protein Details
3. HMP-PP phosphatase
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
Protein Details
4. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
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.