Hmdb loader

Showing metabocard for Trigonelline (HMDB0000875)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:16 UTC
HMDB IDHMDB0000875
Secondary Accession Numbers
  • HMDB00875
Metabolite Identification
Common NameTrigonelline
DescriptionTrigonelline, also known as caffearin or gynesine, belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. It is also found in coffee, where it may help to prevent dental caries by preventing the bacteria Streptococcus mutans from adhering to teeth. Trigonelline is an alkaloid with chemical formula C7H7NO2 and CAS number 535-83-1. Trigonelline is a product of the metabolism of niacin (vitamin B3) which is excreted in the urine. High amounts of trigonelline have been found in arabica coffee, fenugreeks, and common peas. Another foods such as yellow bell peppers, orange bellpeppers and muskmelons also contain trigonelline but in lower concentrations. Trigonelline has also been detected but not quantified in several different foods, such as rices, triticales, alfalfa, cereals and cereal products, and ryes. Trigonelline in the urine is a biomarker for the consumption of coffee, legumes and soy products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000875 (Trigonelline)

  Mrv1652303202019022D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  3  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  CHG  2   2   1  10  -1
M  END
Download

3D MOL for HMDB0000875 (Trigonelline)

HMDB0000875
     RDKit          3D
Trigonelline
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.2900   -0.8452    0.3632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0354   -0.1682    0.1192 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.0669    1.1443   -0.1856 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914    1.8560   -0.4311 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3042    1.1850   -0.3570 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3551   -0.1614   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6109   -0.8924    0.0395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7092   -0.3032   -0.1733 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5478   -2.2406    0.3590 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.1567   -0.7922    0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1284   -0.3720   -0.1821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1737   -1.8758   -0.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5505   -0.9454    1.4138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0338    1.6645   -0.2412 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0876    2.9163   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2554    1.6922   -0.5406 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1606   -1.8619    0.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  2  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
 10 17  1  0
M  CHG  2   2   1   9  -1
M  END
Download

3D SDF for HMDB0000875 (Trigonelline)

  Mrv1652303202019022D          

 10 10  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  3  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  CHG  2   2   1  10  -1
M  END
> <DATABASE_ID>
HMDB0000875

> <DATABASE_NAME>
hmdb

> <SMILES>
C[N+]1=CC=CC(=C1)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H7NO2/c1-8-4-2-3-6(5-8)7(9)10/h2-5H,1H3

> <INCHI_KEY>
WWNNZCOKKKDOPX-UHFFFAOYSA-N

> <FORMULA>
C7H7NO2

> <MOLECULAR_WEIGHT>
137.136

> <EXACT_MASS>
137.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.401438455568746

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methylpyridin-1-ium-3-carboxylate

> <ALOGPS_LOGP>
-3.30

> <JCHEM_LOGP>
-3.5302120628050786

> <ALOGPS_LOGS>
-2.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7829632948236522

> <JCHEM_POLAR_SURFACE_AREA>
44.01

> <JCHEM_REFRACTIVITY>
48.1498

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.23e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
trigonelline

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000875 (Trigonelline)

HMDB0000875
     RDKit          3D
Trigonelline
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.2900   -0.8452    0.3632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0354   -0.1682    0.1192 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.0669    1.1443   -0.1856 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914    1.8560   -0.4311 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3042    1.1850   -0.3570 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3551   -0.1614   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6109   -0.8924    0.0395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7092   -0.3032   -0.1733 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5478   -2.2406    0.3590 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.1567   -0.7922    0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1284   -0.3720   -0.1821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1737   -1.8758   -0.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5505   -0.9454    1.4138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0338    1.6645   -0.2412 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0876    2.9163   -0.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2554    1.6922   -0.5406 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1606   -1.8619    0.4335 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  2  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
 10 17  1  0
M  CHG  2   2   1   9  -1
M  END
Download

PDB for HMDB0000875 (Trigonelline)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
Download

3D PDB for HMDB0000875 (Trigonelline)

COMPND    HMDB0000875
HETATM    1  C1  UNL     1      -2.290  -0.845   0.363  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.035  -0.168   0.119  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -1.067   1.144  -0.186  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.091   1.856  -0.431  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.304   1.185  -0.357  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.355  -0.161  -0.046  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.611  -0.892   0.039  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.709  -0.303  -0.173  1.00  0.00           O  
HETATM    9  O2  UNL     1       2.548  -2.241   0.359  1.00  0.00           O1-
HETATM   10  C7  UNL     1       0.157  -0.792   0.184  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.128  -0.372  -0.182  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.174  -1.876  -0.077  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.550  -0.945   1.414  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.034   1.664  -0.241  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.088   2.916  -0.679  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.255   1.692  -0.541  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.161  -1.862   0.434  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    3   10
CONECT    3    4   14
CONECT    4    5    5   15
CONECT    5    6   16
CONECT    6    7   10   10
CONECT    7    8    8    9
CONECT   10   17
END
Download

SMILES for HMDB0000875 (Trigonelline)

C[N+]1=CC=CC(=C1)C([O-])=O
Download

INCHI for HMDB0000875 (Trigonelline)

InChI=1S/C7H7NO2/c1-8-4-2-3-6(5-8)7(9)10/h2-5H,1H3
Download
View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC7H7NO2
Average Molecular Weight137.136
Monoisotopic Molecular Weight137.047678473
IUPAC Name1-methylpyridin-1-ium-3-carboxylate
Traditional Nametrigonelline
CAS Registry Number535-83-1
SMILES
C[N+]1=CC=CC(=C1)C([O-])=O
InChI Identifier
InChI=1S/C7H7NO2/c1-8-4-2-3-6(5-8)7(9)10/h2-5H,1H3
InChI KeyWWNNZCOKKKDOPX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassNot Available
Sub ClassNot Available
Direct ParentAlkaloids and derivatives
Alternative Parents
Substituents
  • Pyridine carboxylic acid
  • Alkaloid or derivatives
  • Pyridine carboxylic acid or derivatives
  • N-methylpyridinium
  • Pyridinium
  • Pyridine
  • Heteroaromatic compound
  • Vinylogous amide
  • Carboxylic acid salt
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organic salt
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-3.910 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Baker126.36730932474
[M+H]+Not Available124.9http://allccs.zhulab.cn/database/detail?ID=AllCCS00001380
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Lung Cancer
  1. Stretch C, Eastman T, Mandal R, Eisner R, Wishart DS, Mourtzakis M, Prado CM, Damaraju S, Ball RO, Greiner R, Baracos VE: Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. J Nutr. 2012 Jan;142(1):14-21. doi: 10.3945/jn.111.147751. Epub 2011 Dec 7. [PubMed:22157537 ]
Autosomal dominant polycystic kidney disease
  1. Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002237
KNApSAcK IDC00001555
Chemspider ID5369
KEGG Compound IDC01004
BioCyc IDMETHYLNICOTINATE
BiGG IDNot Available
Wikipedia LinkTrigonelline
METLIN ID273
PubChem Compound5570
PDB IDNot Available
ChEBI ID18123
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1698551
References
Synthesis ReferenceSarett, Herbert P.; Perlzweig, William A.; Levy, Edward D. Synthesis and excretion of trigonelline. Journal of Biological Chemistry (1940), 135 483-5.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Nishina Y, Sato K, Miura R, Shiga K: Substrate recognition and activation mechanism of D-amino acid oxidase: a study using substrate analogs. J Biochem. 2000 Aug;128(2):213-23. [PubMed:10920257 ]
  2. Slow S, Miller WE, McGregor DO, Lee MB, Lever M, George PM, Chambers ST: Trigonelline is not responsible for the acute increase in plasma homocysteine following ingestion of instant coffee. Eur J Clin Nutr. 2004 Sep;58(9):1253-6. [PubMed:15054441 ]
  3. Dellow WJ, Chambers ST, Lever M, Lunt H, Robson RA: Elevated glycine betaine excretion in diabetes mellitus patients is associated with proximal tubular dysfunction and hyperglycemia. Diabetes Res Clin Pract. 1999 Feb;43(2):91-9. [PubMed:10221661 ]
  4. Rozan P, Kuo YH, Lambein F: Free amino acids present in commercially available seedlings sold for human consumption. A potential hazard for consumers. J Agric Food Chem. 2000 Mar;48(3):716-23. [PubMed:10725139 ]
  5. Daglia M, Tarsi R, Papetti A, Grisoli P, Dacarro C, Pruzzo C, Gazzani G: Antiadhesive effect of green and roasted coffee on Streptococcus mutans' adhesive properties on saliva-coated hydroxyapatite beads. J Agric Food Chem. 2002 Feb 27;50(5):1225-9. [PubMed:11853508 ]
  6. Tohda C, Kuboyama T, Komatsu K: Search for natural products related to regeneration of the neuronal network. Neurosignals. 2005;14(1-2):34-45. [PubMed:15956813 ]
  7. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]