MiMeDB: Showing metabocard for pyrithiamine (MMDBc0047885)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:47:32 UTC

Update Date

2025-10-07 16:08:09 UTC

Metabolite ID

MMDBc0047885

Metabolite Identification

Common Name

pyrithiamine

Description

Pyrithiamine is a thiamine antimetabolite belonging to the class of chemical compounds known as vitamin B1 analogs. Its chemical structure features a pyrimidine ring, which is essential for its function as an inhibitor of thiamine-dependent enzymes. Pyrithiamine disrupts the biosynthesis of thiamine diphosphate (TDP) by inhibiting thiamine pyrophosphate kinase (TPK), leading to reduced TDP levels in various tissues, including the brain, liver, and kidney (PMID:39190417 ). It is commonly used in experimental models to induce thiamine deficiency, particularly in male rodents, thereby elucidating the biochemical pathways affected by thiamine deprivation (PMID:37684026 ). Studies have shown that pyrithiamine can bind effectively to LdTPK, influencing reactive oxygen species (ROS) defense mechanisms in organisms like Leishmania (PMID:37350670 ). Furthermore, pyrithiamine's role in experimental thiamine deficiency models, such as the Wernicke-Korsakoff syndrome, highlights its impact on cognitive functions and neurotransmitter changes (PMID:36771332 ). Overall, pyrithiamine serves as a critical tool in understanding thiamine metabolism and its associated biological pathways.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572001271616172D          

 19 20  0  0  0  0            999 V2000
    0.7144    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5723   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 12 16  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047885

> <DATABASE_NAME>
MIME

> <SMILES>
CC1N(CC2=CN=C(C)N=C2N)C=CC=C1CCO

> <INCHI_IDENTIFIER>
InChI=1S/C14H20N4O/c1-10-12(5-7-19)4-3-6-18(10)9-13-8-16-11(2)17-14(13)15/h3-4,6,8,10,19H,5,7,9H2,1-2H3,(H2,15,16,17)

> <INCHI_KEY>
UZLPMHGCXVJFGY-UHFFFAOYSA-N

> <FORMULA>
C14H20N4O

> <MOLECULAR_WEIGHT>
260.341

> <EXACT_MASS>
260.16371128

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
29.147902802764413

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-methyl-1,2-dihydropyridin-3-yl}ethan-1-ol

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
0.6675529203333334

> <ALOGPS_LOGS>
-2.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.928080510039916

> <JCHEM_PKA_STRONGEST_BASIC>
6.9551406636612425

> <JCHEM_POLAR_SURFACE_AREA>
75.27000000000001

> <JCHEM_REFRACTIVITY>
79.3315

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-methyl-2H-pyridin-3-yl}ethanol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-JAN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-JAN-16         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -5.335   0.000   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -4.001   0.770   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -4.001   2.310   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.668   0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14                                                            
CONECT   16   12                                                            
CONECT   17    3   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

Synonyms

Value	Source
Pyrithiamin	MetaCyc
Neopyrithiamine	MetaCyc
2-{1-[(4-amino-2-methyl-5-pyrimidinyl)methyl]-2-methyl-1,2-dihydro-3-pyridinyl}ethanol	MetaCyc

Molecular Formula

C₁₄H₂₀N₄O

Average Mass

260.341

Monoisotopic Mass

260.16371128

IUPAC Name

2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-methyl-1,2-dihydropyridin-3-yl}ethan-1-ol

Traditional Name

2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-methyl-2H-pyridin-3-yl}ethanol

CAS Registry Number

Not Available

SMILES

CC1N(CC2=CN=C(C)N=C2N)C=CC=C1CCO

InChI Identifier

InChI=1S/C14H20N4O/c1-10-12(5-7-19)4-3-6-18(10)9-13-8-16-11(2)17-14(13)15/h3-4,6,8,10,19H,5,7,9H2,1-2H3,(H2,15,16,17)

InChI Key

UZLPMHGCXVJFGY-UHFFFAOYSA-N

Chemical Taxonomy

Description

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
Dihydropyridine
Aralkylamine
Hydropyridine
Imidolactam
Heteroaromatic compound
Tertiary amine
Tertiary aliphatic amine
Allylamine
Enamine
Azacycle
Amine
Alcohol
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.62 g/L	ALOGPS
logP	0.97	ALOGPS
logP	0.67	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	15.93	ChemAxon
pKa (Strongest Basic)	6.96	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.27 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	79.33 m³·mol⁻¹	ChemAxon
Polarizability	29.15 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00dj-4970000000-3d9759f9f7c289fe5b2e	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01vo-0290000000-23035b028b180797849a	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-3960000000-9ca45aa703dc32a24ad6	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-5910000000-100c2eb39c59c870dc89	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0190000000-895483ff46d17b245d38	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-1910000000-b5bdda3ce6b4edce65ae	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9610000000-3e3473edec6473b0f802	2016-09-14	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	97.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	145.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	73.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	250.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	279.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	197.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	551.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	657.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	301.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	155.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	360.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	150.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	91.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	227.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	447.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	50.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	196.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	823.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	637.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	pyrithiamine_TMS_1	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N)=N1	standard non polar	2025-10-24	2023.46
Gas Chromatography	pyrithiamine_TMS_2	CC1=NC=C(CN2C=CC=C(CCO)C2C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2115.08
Gas Chromatography	pyrithiamine_TMS_3	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2371.57
Gas Chromatography	pyrithiamine_TMS_4	CC1=NC=C(CN2C=CC=C(CCO)C2C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	2629.45
Gas Chromatography	pyrithiamine_TMS_5	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	2182.47
Gas Chromatography	pyrithiamine_TMS_1	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N)=N1	standard polar	2025-10-24	2135.63
Gas Chromatography	pyrithiamine_TMS_2	CC1=NC=C(CN2C=CC=C(CCO)C2C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2160.97
Gas Chromatography	pyrithiamine_TMS_3	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2381.31
Gas Chromatography	pyrithiamine_TMS_4	CC1=NC=C(CN2C=CC=C(CCO)C2C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1435.71
Gas Chromatography	pyrithiamine_TMS_5	CC1=NC=C(CN2C=CC=C(CCO[Si](C)(C)C)C2C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1390.25

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019944	pyrithiamine	4-Amino-5-hydroxymethyl-2-methylpyrimidine	Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20	Phosphorylation	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

416151

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for pyrithiamine (MMDBc0047885)

MOL for #<Metabolite:0x00007f9af152ef48>

3D MOL for #<Metabolite:0x00007f9af152ef48>

3D SDF for #<Metabolite:0x00007f9af152ef48>

3D-SDF for #<Metabolite:0x00007f9af152ef48>

PDB for #<Metabolite:0x00007f9af152ef48>

3D PDB for #<Metabolite:0x00007f9af152ef48>

SMILES for #<Metabolite:0x00007f9af152ef48>

INCHI for #<Metabolite:0x00007f9af152ef48>

Structure for #<Metabolite:0x00007f9af152ef48>

3D Structure for #<Metabolite:0x00007f9af152ef48>