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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 01:33:11 UTC

Update Date

2023-02-21 17:27:22 UTC

HMDB ID

HMDB0040001

Secondary Accession Numbers

HMDB40001

Metabolite Identification

Common Name

Trimethylpropylpyrazine

Description

Trimethylpropylpyrazine belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. Trimethylpropylpyrazine has been detected, but not quantified in, cocoa and cocoa products and cocoa beans (Theobroma cacao). This could make trimethylpropylpyrazine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Trimethylpropylpyrazine.

Structure

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

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
CONECT    1    5                                                            
CONECT    2    7                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5    1    6                                                       
CONECT    6    5   10                                                       
CONECT    7    2    8   11                                                  
CONECT    8    3    7   12                                                  
CONECT    9    4   10   11                                                  
CONECT   10    6    9   12                                                  
CONECT   11    7    9                                                       
CONECT   12    8   10                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

COMPND    HMDB0040001
HETATM    1  C1  UNL     1      -4.073   0.361   0.292  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.606   0.271   0.658  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.835   0.080  -0.612  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.367  -0.027  -0.404  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.436   1.053  -0.632  1.00  0.00           N  
HETATM    6  C5  UNL     1       1.766   1.011  -0.442  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.616   2.208  -0.700  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.364  -0.147  -0.003  1.00  0.00           C  
HETATM    9  C8  UNL     1       3.830  -0.247   0.226  1.00  0.00           C  
HETATM   10  N2  UNL     1       1.563  -1.200   0.216  1.00  0.00           N  
HETATM   11  C9  UNL     1       0.230  -1.189   0.035  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.537  -2.433   0.302  1.00  0.00           C  
HETATM   13  H1  UNL     1      -4.633  -0.301   0.987  1.00  0.00           H  
HETATM   14  H2  UNL     1      -4.494   1.380   0.430  1.00  0.00           H  
HETATM   15  H3  UNL     1      -4.257   0.106  -0.781  1.00  0.00           H  
HETATM   16  H4  UNL     1      -2.277   1.263   1.079  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.384  -0.529   1.355  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.061   0.955  -1.278  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.210  -0.808  -1.197  1.00  0.00           H  
HETATM   20  H8  UNL     1       3.251   2.023  -1.598  1.00  0.00           H  
HETATM   21  H9  UNL     1       1.993   3.087  -0.953  1.00  0.00           H  
HETATM   22  H10 UNL     1       3.228   2.467   0.186  1.00  0.00           H  
HETATM   23  H11 UNL     1       4.304   0.734   0.318  1.00  0.00           H  
HETATM   24  H12 UNL     1       4.016  -0.926   1.082  1.00  0.00           H  
HETATM   25  H13 UNL     1       4.260  -0.784  -0.664  1.00  0.00           H  
HETATM   26  H14 UNL     1      -0.134  -3.249  -0.375  1.00  0.00           H  
HETATM   27  H15 UNL     1      -0.393  -2.798   1.336  1.00  0.00           H  
HETATM   28  H16 UNL     1      -1.596  -2.361   0.091  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   16   17
CONECT    3    4   18   19
CONECT    4    5    5   11
CONECT    5    6
CONECT    6    7    8    8
CONECT    7   20   21   22
CONECT    8    9   10
CONECT    9   23   24   25
CONECT   10   11   11
CONECT   11   12
CONECT   12   26   27   28
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,3,5-Trimethyl-6-propylpyrazine	HMDB
2-Propyl-3,5,6-trimethylpyrazine	HMDB

Chemical Formula

C₁₀H₁₆N₂

Average Molecular Weight

164.2474

Monoisotopic Molecular Weight

164.131348522

IUPAC Name

2,3,5-trimethyl-6-propylpyrazine

Traditional Name

2,3,5-trimethyl-6-propylpyrazine

CAS Registry Number

92233-82-4

SMILES

CCCC1=C(C)N=C(C)C(C)=N1

InChI Identifier

InChI=1S/C10H16N2/c1-5-6-10-9(4)11-7(2)8(3)12-10/h5-6H2,1-4H3

InChI Key

GEPYSCIASYXPCY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0040001)
Cytoplasm (HMDB: HMDB0040001)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0040001)

Source

Exogenous

Exogenous (HMDB: HMDB0040001)

Food

Food (HMDB: HMDB0040001)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Cocoa and cocoa products (FooDB: FOOD00860)

Endogenous

Plant

Theobroma cacao (HMDB: HMDB0040001)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0040001)

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	144 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.07 g/L	ALOGPS
logP	2.45	ALOGPS
logP	1.21	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Basic)	2.07	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	25.78 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	49.34 m³·mol⁻¹	ChemAxon
Polarizability	20.04 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	135.466	31661259
DarkChem	[M-H]-	134.998	31661259
DeepCCS	[M+H]+	143.283	30932474
DeepCCS	[M-H]-	139.456	30932474
DeepCCS	[M-2H]-	176.786	30932474
DeepCCS	[M+Na]+	152.348	30932474
AllCCS	[M+H]+	136.6	32859911
AllCCS	[M+H-H2O]+	132.4	32859911
AllCCS	[M+NH4]+	140.7	32859911
AllCCS	[M+Na]+	141.8	32859911
AllCCS	[M-H]-	141.6	32859911
AllCCS	[M+Na-2H]-	143.0	32859911
AllCCS	[M+HCOO]-	144.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.21 minutes	32390414
Predicted by Siyang on May 30, 2022	9.4414 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.97 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	133.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	549.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	283.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	124.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	157.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	61.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	324.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	292.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	570.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	729.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	194.0 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1277.2 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	210.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	256.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	478.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	474.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	246.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Trimethylpropylpyrazine	CCCC1=C(C)N=C(C)C(C)=N1	1558.0	Standard polar	33892256
Trimethylpropylpyrazine	CCCC1=C(C)N=C(C)C(C)=N1	1191.4	Standard non polar	33892256
Trimethylpropylpyrazine	CCCC1=C(C)N=C(C)C(C)=N1	1236.4	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Trimethylpropylpyrazine GC-MS (Non-derivatized) - 70eV, Positive	splash10-002s-5900000000-4b0c49c01aee11df0047	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Trimethylpropylpyrazine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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 - Trimethylpropylpyrazine 10V, Positive-QTOF	splash10-014i-0900000000-2bf828da56ca40d3f578	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 20V, Positive-QTOF	splash10-014i-0900000000-cf3f2664e13c34f4fe9f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 40V, Positive-QTOF	splash10-000x-9300000000-07d80ab65984cb1fbccc	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 10V, Negative-QTOF	splash10-03di-0900000000-a0e77bfc61ce43eb37b9	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 20V, Negative-QTOF	splash10-03di-0900000000-ecc391f9a14fa88ce8c8	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 40V, Negative-QTOF	splash10-0feb-4900000000-56de73c4909d6384510f	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 10V, Negative-QTOF	splash10-03di-0900000000-bc52f4132052bb241368	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 20V, Negative-QTOF	splash10-03di-0900000000-d9487e8ebbe5c458d96a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 40V, Negative-QTOF	splash10-0002-3900000000-503164494d86b2fb30d7	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 10V, Positive-QTOF	splash10-014i-0900000000-bb7813ae803517e67e94	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 20V, Positive-QTOF	splash10-014i-1900000000-7e84083dace8838da4d5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Trimethylpropylpyrazine 40V, Positive-QTOF	splash10-07c7-9400000000-22afb628594e1593f42f	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB019683

KNApSAcK ID

Not Available

Chemspider ID

509383

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

586005

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1630141

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Trimethylpropylpyrazine (HMDB0040001)

MOL for HMDB0040001 (Trimethylpropylpyrazine)

3D MOL for HMDB0040001 (Trimethylpropylpyrazine)

3D SDF for HMDB0040001 (Trimethylpropylpyrazine)

3D-SDF for HMDB0040001 (Trimethylpropylpyrazine)

PDB for HMDB0040001 (Trimethylpropylpyrazine)

3D PDB for HMDB0040001 (Trimethylpropylpyrazine)

SMILES for HMDB0040001 (Trimethylpropylpyrazine)

INCHI for HMDB0040001 (Trimethylpropylpyrazine)

Structure for HMDB0040001 (Trimethylpropylpyrazine)

3D Structure for HMDB0040001 (Trimethylpropylpyrazine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra