ECMDB: 4-Amino-2-methyl-5-phosphomethylpyrimidine (ECMDB20084) (M2MDB000932)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (5)XML

Proteins (597)

Record Information

Version

2.0

Creation Date

2012-05-31 14:26:35 -0600

Update Date

2015-10-15 16:14:23 -0600

Secondary Accession Numbers

ECMDB20084

Identification

Name:

4-Amino-2-methyl-5-phosphomethylpyrimidine

Description

4-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

MOL SDF PDB SMILES InChI

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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Aminopyrimidines 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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:18032 )
monoalkyl phosphate (CHEBI:18032 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.76 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-1.8	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	1.62	ChemAxon
pKa (Strongest Basic)	7.59	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	58.83 m³·mol⁻¹	ChemAxon
Polarizability	18.83 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Not Available

KEGG Pathways:

Metabolic pathways eco01100
Thiamine metabolism ec00730

EcoCyc Pathways:

4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis PWY-6890

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-006t-9620000000-67208cb5c399d7eb0927	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-1690000000-b4b286e97e3c3859ded5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-2900000000-ef20fcb4606f47d76648	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00ea-9400000000-23f2dc587b8ee21085af	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-016s-9080000000-bb863e533b4baa6368fd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-f35dbb3f524d9e7e08e0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-04a487a0ef46589c29a0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-0490000000-d0df918acbe4ba0a1686	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00e9-8900000000-4224a9cd25055b1596c1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0560-9200000000-d4f98d693c874da458ad	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9010000000-28b8f8a4523c0b4ca1a8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View 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

Links

External Links:

Resource	Link
CHEBI ID	18032
HMDB ID	HMDB0243613
Pubchem Compound ID	216
Kegg ID	C04556
ChemSpider ID	211
Wikipedia ID	Not Available
BioCyc ID	AMINO-HYDROXYMETHYL-METHYL-PYR-P
EcoCyc ID	AMINO-HYDROXYMETHYL-METHYL-PYR-P
Ligand Expo	MP5

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. Pyridoxine kinase

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.

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.

Protein Details

5. Phosphomethylpyrimidine synthase

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.

4-Amino-2-methyl-5-phosphomethylpyrimidine (ECMDB20084) (M2MDB000932)

Structure for #<Compound:0xafb3be38>

Enzymes

Reactions

Reactions

Reactions