P. aeruginosa Metabolome Database: 4-Amino-5-hydroxymethyl-2-methylpyrimidine (PAMDB000934)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000934

Identification

Name:

4-Amino-5-hydroxymethyl-2-methylpyrimidine

Description:

4-amino-5-hydroxymethyl-2-methylpyrimidine 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. The conversion of 5-aminoimidazole ribonucleotide (AIR) into 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) is a fascinating reaction on the thiamin biosynthetic pathway in bacteria and is probably the most complex unresolved rearrangement in primary metabolism. (PMID 15326535)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

(4-Amino-2-methyl-5-pyrimidinyl)methanol
(4-amino-2-methylpyrimidin-5-yl)methanol
2-M-4-A-5-Hmp
2-Methyl-4-amino-5-hydroxymethylpyrimidine
4-Amino-2-methyl-5-hydroxymethylpyrimidine
4-Amino-2-methyl-5-pyrimidinemethanol
4-amino-5-hydroxymethyl-2-methylpyrimidine
5-Pyrimidinemethanol, 4-amino-2-methyl- (8CI)(9CI)
6-Amino-5-hydroxymethyl-2-methylpyrimidine
Atoxopyrimidine
HMePyr
HMH
HMP
Hydroxymethylpyrimidine
Nchembio.121-comp11
NChemBio.2007.13-comp6
OMPM
Oxymethylpyrimidine
Pyramin
Pyramin (van)
Pyramine
Pyramine (thiamine metabolite)
Pyramine (van)
Pyrazan
Toxopyrimidine
TXP

Chemical Formula:

C₆H₉N₃O

Average Molecular Weight:

139.1552

Monoisotopic Molecular Weight:

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)

CAS number:

73-67-6

IUPAC Name:

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

Traditional IUPAC Name:

toxopyrimidine

SMILES:

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

Chemical Taxonomy

Taxonomy Description

This compound 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
Imidolactam
Primary aromatic amine
Heteroaromatic compound
Azacycle
Hydrocarbon derivative
Aromatic alcohol
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
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	Source

Predicted Properties

Property	Value	Source
Water Solubility	12.0 mg/mL	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

Reactions:

4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <> 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine <> ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine
4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <> 5-Aminoimidazole ribonucleotide + 4-Amino-2-methyl-5-phosphomethylpyrimidine + 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine <> Hydrogen ion + ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine

Pathways:

ABC transporters pae02010
Metabolic pathways pae01100
Thiamine metabolism pae00730

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-006x-0900000000-1464721132642f06c763	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-1900000000-ffcb98d194c46375afed	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-007k-9200000000-146c29035e7732b4a386	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0900000000-a6fee6edf0aa915e501a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4r-4900000000-7fb22624813fc7a88208	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-fd0e2a1b16eb26493e89	View in MoNA

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
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
Lawhorn, B. G., Mehl, R. A., Begley, T. P. (2004). "Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction." Org Biomol Chem 2:2538-2546. Pubmed: 15326535
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	16892
HMDB ID	Not Available
Pubchem Compound ID	777
Kegg ID	C01279
ChemSpider ID	756
Wikipedia ID	Not Available
BioCyc ID	HMP
EcoCyc ID	HMP
Ligand Expo	HMH

4-Amino-5-hydroxymethyl-2-methylpyrimidine (PAMDB000934)

Structure for 4-Amino-5-hydroxymethyl-2-methylpyrimidine (PAMDB000934)