4-amino-5-hydroxymethyl-2-methylpyrimidine (YMDB00118)

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Identification

YMDB ID

YMDB00118

Name

4-amino-5-hydroxymethyl-2-methylpyrimidine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

4-Amino-5-hydroxymethyl-2-methylpyrimidine, also known as toxopyrimidine or pyramine, belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.). In yeast, 4-amino-5-hydroxymethyl-2-methylpyrimidine is involved in the metabolic pathway called the vitamin b1/thiamine metabolism pathway. Based on a literature review a significant number of articles have been published on 4-Amino-5-hydroxymethyl-2-methylpyrimidine.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(4-amino-2-methyl-5-pyrimidinyl)methanol
4-amino-2-methyl-5-hydroxymethylpyrimidine
4-Amino-2-methyl-5-pyrimidinemethanol
4-Amino-5-hydroxymethyl-2-methylpyrimidine
5-Pyrimidinemethanol, 4-amino-2-methyl-
Atoxopyrimidine
OMPM
Pyramin (VAN)
Pyramine
Pyramine (thiamine metabolite)
Pyramine (VAN)
Pyrazan
Toxopyrimidine
TXP
2-Methyl-4-amino-5-hydroxymethylpyrimidine
Pyramin
HMP
HMP CPD

CAS number

73-67-6

Weight

Average: 139.1552
Monoisotopic: 139.074561925

InChI Key

VUTBELPREDJDDH-UHFFFAOYSA-N

InChI

InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)

IUPAC Name

(4-amino-2-methylpyrimidin-5-yl)methanol

Traditional IUPAC Name

toxopyrimidine

Chemical Formula

C₆H₉N₃O

SMILES

CC1=NC=C(CO)C(N)=N1

Chemical Taxonomy

Description

belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Hydropyrimidines

Alternative Parents

Substituents

Imidolactam
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:16892 )
aromatic primary alcohol (CHEBI:16892 )
a small molecule (HMP )

Physical Properties

State

Solid

Charge

Melting point

198 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	12 g/L	ALOGPS
logP	-0.26	ALOGPS
logP	-0.36	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	14.41	ChemAxon
pKa (Strongest Basic)	6.17	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	72.03 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	39.18 m³·mol⁻¹	ChemAxon
Polarizability	14.2 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

Organoleptic Properties

Not Available

SMPDB Pathways

Vitamin B1/Thiamine metabolism

PW002486

KEGG Pathways

Thiamine metabolism

ec00730

SMPDB Reactions

Adenosine triphosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine → 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP

4-amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate ADP + hydron + 4-amino-2-methyl-5-phosphomethylpyrimidine

pyrithiamine + water + oxidized electron acceptor → 4-amino-5-hydroxymethyl-2-methylpyrimidine + 2-(2-methylpyridin-3-yl)ethanol + reduced electron acceptor

KEGG Reactions

5-Aminoimidazole ribonucleotide + hydron → Glycolaldehyde + phosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine

Adenosine triphosphate + 4-amino-5-hydroxymethyl-2-methylpyrimidine → 4-amino-2-methyl-5-phosphomethylpyrimidine + hydron + ADP

Thiamine + water → hydron + 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-Hydroxyethyl)-4-methylthiazole

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0abi-1900000000-e3106b1f3a699dcbb5cf	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006x-0900000000-1464721132642f06c763	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-1900000000-ffcb98d194c46375afed	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-007k-9200000000-146c29035e7732b4a386	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-a6fee6edf0aa915e501a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4r-4900000000-7fb22624813fc7a88208	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-fd0e2a1b16eb26493e89	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dl-0900000000-bcee92b22282400d9aa9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00e9-7900000000-c3b2ba29d4a3384fbf9f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00lu-9000000000-cecde0be355431a2920b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-cfc1d884f8ea3db6b6a6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-006x-8900000000-bb08081d11c0ce993537	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-014l-9000000000-f27a78acaec6ce875983	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer

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
Kawasaki, Y., Onozuka, M., Mizote, T., Nosaka, K. (2005). "Biosynthesis of hydroxymethylpyrimidine pyrophosphate in Saccharomyces cerevisiae." Curr Genet 47:156-162.15614489
Onozuka, M., Konno, H., Kawasaki, Y., Akaji, K., Nosaka, K. (2008). "Involvement of thiaminase II encoded by the THI20 gene in thiamin salvage of Saccharomyces cerevisiae." FEMS Yeast Res 8:266-275.18028398
Kawasaki, Y., Nosaka, K., Kaneko, Y., Nishimura, H., Iwashima, A. (1990). "Regulation of thiamine biosynthesis in Saccharomyces cerevisiae." J Bacteriol 172:6145-6147.2170344

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	16892
HMDB ID	HMDB0247327
Pubchem Compound ID	777
Kegg ID	C01279
ChemSpider ID	756
FOODB ID	FDB030912
Wikipedia ID	4-Amino-5-hydroxymethyl-2-methylpyrimidine
BioCyc ID	Not Available

Enzymes

Protein Details

1. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI21

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.

Protein Details

2. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20

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.

Protein Details

3. Thiamine biosynthesis protein THI22

General function:: Coenzyme transport and metabolism
Specific function:: Essential for thiamine biosynthesis
Gene Name:: THI22
Uniprot ID:: Q06490
Molecular weight:: 63306.39844

Reactions

4-amino-5-hydroxymethyl-2-methylpyrimidine (YMDB00118)

Structure for #<Compound:0xb17adda0>

Enzymes

Reactions

Reactions

Reactions