2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (PAMDB000895)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000895
Identification
Name: 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
Description:2-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
🔍MOLSDFPDBSMILESInChIView Structure
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
Average Molecular Weight: 296.093
Monoisotopic Molecular Weight: 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
Taxonomy DescriptionThis compound 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.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Organic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct Parent Organic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organonitrogen compound
  • Amine
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility12.2 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity66.33 m3·mol-1ChemAxon
Polarizability22.61 Å3ChemAxon
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
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
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
Pathways:
Spectra
Spectra:
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 IDNot Available
Pubchem Compound ID217
Kegg IDC04752
ChemSpider ID212
Wikipedia IDNot Available
BioCyc IDAMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP
EcoCyc IDAMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP