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Record Information
Version	2.0
Creation Date	2012-05-31 14:26:41 -0600
Update Date	2015-06-03 17:19:17 -0600
Secondary Accession Numbers	ECMDB20086
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	MOLSDFPDBSMILESInChI × Structure for #<Compound:0xa3859b54> Close
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
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)
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
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	Imidolactams Heteroaromatic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Hydrocarbon derivatives Aromatic alcohols
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:	0
Melting point:	198 °C
Experimental Properties:	Property Value Source
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 Ų ChemAxon Rotatable Bond Count 1 ChemAxon Refractivity 39.18 m³·mol⁻¹ ChemAxon Polarizability 14.2 ų 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 Adenosine triphosphate + 4-Amino-5-hydroxymethyl-2-methylpyrimidine > ADP + 4-Amino-2-methyl-5-phosphomethylpyrimidine 4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <>4 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion +4 4-amino-5-phosphonooxymethyl-2-methylpyrimidine 4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <>5 5-Aminoimidazole ribonucleotide +4 4-Amino-2-methyl-5-phosphomethylpyrimidine +5 5'-Deoxyadenosine + L-Methionine + Formic acid + CO 4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + Adenosine triphosphate <>4 4-Amino-2-methyl-5-phosphomethylpyrimidine + ADP + Hydrogen ion +4 4-amino-5-phosphonooxymethyl-2-methylpyrimidine 4 4-Amino-5-hydroxymethyl-2-methylpyrimidine + S-Adenosylmethionine <>5 5-Aminoimidazole ribonucleotide +4 4-Amino-2-methyl-5-phosphomethylpyrimidine +5 5'-Deoxyadenosine + L-Methionine + Formic acid + CO
SMPDB Pathways:	Not Available
KEGG Pathways:	ABC transporters ec02010 Metabolic pathways eco01100 Thiamine metabolism ec00730
EcoCyc Pathways:	Not Available
Concentrations
	Not Available
Spectra
Spectra:	Spectrum Type Description Splash Key Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive splash10-0abi-1900000000-e3106b1f3a699dcbb5cf View in MoNA Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive Not Available View in JSpectraViewer Predicted GC-MS Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive Not Available View in JSpectraViewer 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 Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-00dl-0900000000-bcee92b22282400d9aa9 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-00e9-7900000000-c3b2ba29d4a3384fbf9f View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-00lu-9000000000-cecde0be355431a2920b View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-000i-0900000000-cfc1d884f8ea3db6b6a6 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-006x-8900000000-bb08081d11c0ce993537 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-014l-9000000000-f27a78acaec6ce875983 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 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 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H 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
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 HMDB0247327 Pubchem Compound ID 777 Kegg ID C01279 ChemSpider ID 756 Wikipedia ID 4-Amino-5-hydroxymethyl-2-methylpyrimidine BioCyc ID HMP EcoCyc ID HMP Ligand Expo HMH

Enzymes