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Identification
YMDB IDYMDB00117
Name4-amino-2-methyl-5-diphosphomethylpyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description4-Amino-2-methyl-5-diphosphomethylpyrimidine is an intermediate in thiamine biosynthesis. [Biocyc THISYNARA-PWY]
Structure
Thumb
Synonyms
  • (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
  • 4-Amino-2-methyl-5-diphosphomethylpyrimidine
  • (4-amino-2-Methylpyrimidin-5-yl)methyl diphosphoric acid
  • 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphoric acid
CAS numberNot Available
WeightAverage: 299.115
Monoisotopic: 299.007222745
InChI KeyAGQJQCFEPUVXNK-UHFFFAOYSA-N
InChIInChI=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)
IUPAC Name({hydroxy[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphoryl}oxy)phosphonic acid
Traditional IUPAC Name[hydroxy(4-imino-2-methyl-3H-pyrimidin-5-yl)methoxyphosphoryl]oxyphosphonic acid
Chemical FormulaC6H11N3O7P2
SMILESCC1=NC=C(COP(O)(=O)OP(O)(O)=O)C(N)=N1
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganic oxoanionic compounds
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Azacycle
  • Organoheterocyclic compound
  • Primary amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • 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 Solubility3.37 g/LALOGPS
logP-0.58ALOGPS
logP-2.8ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)7.17ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area161.53 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity69.7 m³·mol⁻¹ChemAxon
Polarizability23.48 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
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + hydronThiamine monophosphate + Carbon dioxide + diphosphate
Pyridoxal 5'-phosphate4-amino-2-methyl-5-diphosphomethylpyrimidine
Adenosine triphosphate + 4-amino-2-methyl-5-phosphomethylpyrimidineADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
4-amino-2-methyl-5-diphosphomethylpyrimidine + hydron + 4-methyl-5-(2-phosphonooxyethyl)thiazole → Pyrophosphate + Thiamine monophosphate
KEGG Reactions
4-amino-2-methyl-5-phosphomethylpyrimidine + Adenosine triphosphate4-amino-2-methyl-5-diphosphomethylpyrimidine + ADP
4-Methyl-5-(2-phosphonooxyethyl)thiazole + hydron + 4-amino-2-methyl-5-diphosphomethylpyrimidinePyrophosphate + Thiamine monophosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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
  • 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 ID16629
HMDB IDNot Available
Pubchem Compound ID217
Kegg IDC04752
ChemSpider ID212
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

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.
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.
General function:
Involved in catalytic activity
Specific function:
Essential for thiamine biosynthesis. The kinase activity is involved in the salvage synthesis of TH-P from the thiazole
Gene Name:
THI6
Uniprot ID:
P41835
Molecular weight:
58058.19922
Reactions
2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate + 4-methyl-5-(2-phosphono-oxyethyl)thiazole → diphosphate + thiamine phosphate.
ATP + 4-methyl-5-(2-hydroxyethyl)thiazole → ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole.
General function:
Coenzyme transport and metabolism
Specific function:
Essential for thiamine biosynthesis
Gene Name:
THI22
Uniprot ID:
Q06490
Molecular weight:
63306.39844
Reactions