Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:20:00 UTC
Update Date2021-10-01 18:58:20 UTC
HMDB IDHMDB0247327
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Amino-5-hydroxymethyl-2-methylpyrimidine
Description4-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.). 4-Amino-5-hydroxymethyl-2-methylpyrimidine has been detected, but not quantified in, several different foods, such as dates (Phoenix dactylifera), mamey sapotes (Pouteria sapota), pepper (spice), allspices (Pimenta dioica), and common sages (Salvia officinalis). This could make 4-amino-5-hydroxymethyl-2-methylpyrimidine a potential biomarker for the consumption of these foods. 4-Amino-5-hydroxymethyl-2-methylpyrimidine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on 4-Amino-5-hydroxymethyl-2-methylpyrimidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-amino-5-hydroxymethyl-2-methylpyrimidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Amino-5-hydroxymethyl-2-methylpyrimidine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
2-Methyl-4-amino-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-pyrimidinemethanolChEBI
AtoxopyrimidineChEBI
PyraminChEBI
PyramineChEBI
ToxopyrimidineChEBI
HMPKegg
HMP CPDHMDB
Chemical FormulaC6H9N3O
Average Molecular Weight139.1552
Monoisotopic Molecular Weight139.074561925
IUPAC Name(4-amino-2-methylpyrimidin-5-yl)methanol
Traditional Nametoxopyrimidine
CAS Registry NumberNot Available
SMILES
CC1=NC=C(CO)C(N)=N1
InChI Identifier
InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
InChI KeyVUTBELPREDJDDH-UHFFFAOYSA-N
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.).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydropyrimidines
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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP10(-0.26) g/LALOGPS
logP10(-0.36) g/LChemAxon
logS10(-1.1) g/LALOGPS
pKa (Strongest Acidic)14.41ChemAxon
pKa (Strongest Basic)6.17ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.18 m³·mol⁻¹ChemAxon
Polarizability14.2 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+134.08530932474
DeepCCS[M-H]-130.29630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-Amino-5-hydroxymethyl-2-methylpyrimidineCC1=NC=C(CO)C(N)=N12426.8Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidineCC1=NC=C(CO)C(N)=N11463.7Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidineCC1=NC=C(CO)C(N)=N11480.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N11621.5Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N11605.1Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N12181.9Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N11635.6Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N11791.1Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N12161.1Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N11682.8Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N11747.6Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TMS,isomer #1CC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N11946.3Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N12089.3Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N11996.5Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N12367.1Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12067.5Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12191.7Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,2TBDMS,isomer #2CC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12287.1Standard polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12283.4Semi standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12349.0Standard non polar33892256
4-Amino-5-hydroxymethyl-2-methylpyrimidine,3TBDMS,isomer #1CC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N12280.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0abi-1900000000-e3106b1f3a699dcbb5cf2016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 10V, Positive-QTOFsplash10-006x-0900000000-1464721132642f06c7632015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 20V, Positive-QTOFsplash10-00di-1900000000-ffcb98d194c46375afed2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 40V, Positive-QTOFsplash10-007k-9200000000-146c29035e7732b4a3862015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 10V, Negative-QTOFsplash10-000i-0900000000-a6fee6edf0aa915e501a2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 20V, Negative-QTOFsplash10-0a4r-4900000000-7fb22624813fc7a882082015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 40V, Negative-QTOFsplash10-0006-9000000000-fd0e2a1b16eb26493e892015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 10V, Positive-QTOFsplash10-00dl-0900000000-bcee92b22282400d9aa92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 20V, Positive-QTOFsplash10-00e9-7900000000-c3b2ba29d4a3384fbf9f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 40V, Positive-QTOFsplash10-00lu-9000000000-cecde0be355431a2920b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 10V, Negative-QTOFsplash10-000i-0900000000-cfc1d884f8ea3db6b6a62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 20V, Negative-QTOFsplash10-006x-8900000000-bb08081d11c0ce9935372021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-Amino-5-hydroxymethyl-2-methylpyrimidine 40V, Negative-QTOFsplash10-014l-9000000000-f27a78acaec6ce8759832021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02022
Phenol Explorer Compound IDNot Available
FooDB IDFDB030912
KNApSAcK IDC00007494
Chemspider ID756
KEGG Compound IDC01279
BioCyc IDHMP
BiGG IDNot Available
Wikipedia Link4-Amino-5-hydroxymethyl-2-methylpyrimidine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16892
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1376481
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

General function:
Not Available
Specific function:
Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway. Thus, catalyzes the conversion of 4-amino-5-aminomethyl-2-methylpyrimidine to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). Is also able to catalyze the hydrolytic cleavage of thiamine; however, this thiaminase activity may not be physiologically relevant. Therefore, is probably involved in the regeneration of the thiamine pyrimidine from thiamine degraded products present in the environment, rather than in thiamine degradation.
Gene Name:
TENA
Uniprot ID:
Q4L7X6
Molecular weight:
26675.81
General function:
Not Available
Specific function:
Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds to give a hydroxymethylpyrimidine (HMP). Displays low activity on 4-amino-5-aminomethyl-2-methylpyrimidine as substrate, indicating that the enzyme may act on a different HMP precursor that may derive from the human stomach food assumption or processing. Is probably involved in thiamine biosynthesis. Does not display thiaminase II activity, as it is unable to hydrolyze thiamine.
Gene Name:
TENA
Uniprot ID:
A8KRL3
Molecular weight:
25012.31
General function:
Not Available
Specific function:
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P.
Gene Name:
THID
Uniprot ID:
Q9ZL00
Molecular weight:
28768.17