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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 00:00:52 UTC

Update Date

2021-09-26 22:56:25 UTC

HMDB ID

HMDB0246995

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Methioprim

Description

[6-imino-2-(methylsulfanyl)-1,6-dihydropyrimidin-5-yl]methanol belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group. Based on a literature review very few articles have been published on [6-imino-2-(methylsulfanyl)-1,6-dihydropyrimidin-5-yl]methanol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methioprim is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methioprim 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
[6-Imino-2-(methylsulphanyl)-1,6-dihydropyrimidin-5-yl]methanol	Generator
5-((3,5-Dimethoxy-4-(methylthio)phenyl)methyl)-2,4-pyrimidinediamine	MeSH
Metioprim	MeSH

Chemical Formula

C₆H₉N₃OS

Average Molecular Weight

171.22

Monoisotopic Molecular Weight

171.046633096

IUPAC Name

[4-amino-2-(methylsulfanyl)pyrimidin-5-yl]methanol

Traditional Name

[4-amino-2-(methylsulfanyl)pyrimidin-5-yl]methanol

CAS Registry Number

Not Available

SMILES

CSC1=NC=C(CO)C(N)=N1

InChI Identifier

InChI=1S/C6H9N3OS/c1-11-6-8-2-4(3-10)5(7)9-6/h2,10H,3H2,1H3,(H2,7,8,9)

InChI Key

XLVOWGDFXAVSFE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aryl thioethers. These are organosulfur compounds containing a thioether group that is substituted by an aryl group.

Kingdom

Organic compounds

Super Class

Organosulfur compounds

Class

Thioethers

Sub Class

Aryl thioethers

Direct Parent

Aryl thioethers

Alternative Parents

Substituents

Aryl thioether
Aminopyrimidine
Alkylarylthioether
Pyrimidine
Imidolactam
Heteroaromatic compound
Sulfenyl compound
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Alcohol
Aromatic alcohol
Organic oxygen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	0.32	ALOGPS
logP	0.35	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	14.35	ChemAxon
pKa (Strongest Basic)	5.41	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	2	ChemAxon
Refractivity	47.26 m³·mol⁻¹	ChemAxon
Polarizability	17.18 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	139.686	30932474
DeepCCS	[M-H]-	135.859	30932474
DeepCCS	[M-2H]-	173.286	30932474
DeepCCS	[M+Na]+	148.843	30932474
AllCCS	[M+H]+	136.9	32859911
AllCCS	[M+H-H2O]+	132.7	32859911
AllCCS	[M+NH4]+	140.9	32859911
AllCCS	[M+Na]+	142.0	32859911
AllCCS	[M-H]-	135.8	32859911
AllCCS	[M+Na-2H]-	137.3	32859911
AllCCS	[M+HCOO]-	139.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methioprim	CSC1=NC=C(CO)C(N)=N1	2700.9	Standard polar	33892256
Methioprim	CSC1=NC=C(CO)C(N)=N1	1727.0	Standard non polar	33892256
Methioprim	CSC1=NC=C(CO)C(N)=N1	1874.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Methioprim,2TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N1	1884.1	Semi standard non polar	33892256
Methioprim,2TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N1	1769.4	Standard non polar	33892256
Methioprim,2TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N[Si](C)(C)C)=N1	2525.8	Standard polar	33892256
Methioprim,2TMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	1868.4	Semi standard non polar	33892256
Methioprim,2TMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	1930.0	Standard non polar	33892256
Methioprim,2TMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	2516.1	Standard polar	33892256
Methioprim,3TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	1907.1	Semi standard non polar	33892256
Methioprim,3TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	1919.6	Standard non polar	33892256
Methioprim,3TMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	2222.2	Standard polar	33892256
Methioprim,2TBDMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N1	2313.4	Semi standard non polar	33892256
Methioprim,2TBDMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N1	2232.3	Standard non polar	33892256
Methioprim,2TBDMS,isomer #1	CSC1=NC=C(CO[Si](C)(C)C(C)(C)C)C(N[Si](C)(C)C(C)(C)C)=N1	2655.5	Standard polar	33892256
Methioprim,2TBDMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	2332.7	Semi standard non polar	33892256
Methioprim,2TBDMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	2373.4	Standard non polar	33892256
Methioprim,2TBDMS,isomer #2	CSC1=NC=C(CO)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=N1	2588.8	Standard polar	33892256
Methioprim,3TBDMS,isomer #1	CSC1=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)=N1	2515.7	Semi standard non polar	33892256
Methioprim,3TBDMS,isomer #1	CSC1=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)=N1	2562.1	Standard non polar	33892256
Methioprim,3TBDMS,isomer #1	CSC1=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)=N1	2524.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fkc-2900000000-35ea5d3a0caf630129c4	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Methioprim GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 10V, Positive-QTOF	splash10-00di-0900000000-3c75ff81794e7bc06e00	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 20V, Positive-QTOF	splash10-0uk9-1900000000-aa96e26d665b4991e665	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 40V, Positive-QTOF	splash10-024l-9200000000-f173d4eb52729aa2a239	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 10V, Negative-QTOF	splash10-00di-0900000000-eba6fecf47920663898c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 20V, Negative-QTOF	splash10-0002-9000000000-e1d92d2a30bee517d754	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Methioprim 40V, Negative-QTOF	splash10-00kb-9000000000-444264b387f23cbe3632	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

191261

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Methioprim (HMDB0246995)

MOL for HMDB0246995 (Methioprim)

3D MOL for HMDB0246995 (Methioprim)

3D SDF for HMDB0246995 (Methioprim)

3D-SDF for HMDB0246995 (Methioprim)

PDB for HMDB0246995 (Methioprim)

3D PDB for HMDB0246995 (Methioprim)

SMILES for HMDB0246995 (Methioprim)

INCHI for HMDB0246995 (Methioprim)

Structure for HMDB0246995 (Methioprim)

3D Structure for HMDB0246995 (Methioprim)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra