Showing NP-Card for Trigonelline (NP0000018)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:49:03 UTC
NP-MRD IDNP0000018
Natural Product DOIhttps://doi.org/10.57994/0677
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000018 (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 NP0000018 (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 NP0000018 (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>
NP0000018

> <DATABASE_NAME>
NP-MRD

> <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 NP0000018 (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 NP0000018 (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
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3D PDB for NP0000018 (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
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SMILES for NP0000018 (Trigonelline)

C[N+]1=CC=CC(=C1)C([O-])=O
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INCHI for NP0000018 (Trigonelline)

InChI=1S/C7H7NO2/c1-8-4-2-3-6(5-8)7(9)10/h2-5H,1H3
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View in JSmol
Synonyms
Chemical FormulaC7H7NO2
Average Mass137.1360 Da
Monoisotopic Mass137.04768 Da
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
Experimental Spectra
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.133705802, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-27View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Eusynstyela latericiusKNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point218 °Chttps://pubchem.ncbi.nlm.nih.gov/compound/Trigonelline#section=Melting-Point
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLhttps://pubchem.ncbi.nlm.nih.gov/compound/Trigonelline#section=Solubility
LogP-2.53https://pubchem.ncbi.nlm.nih.gov/compound/Trigonelline#section=LogP
Predicted Properties
PropertyValueSource
Water Solubility0.32 g/LALOGPS
logP-3.3ALOGPS
logP-3.5ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)2.78ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area44.01 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity48.15 m³·mol⁻¹ChemAxon
Polarizability13.4 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000875
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB002237
KNApSAcK IDC00001555
Chemspider ID5369
KEGG Compound IDC01004
BioCyc IDMETHYLNICOTINATE
BiGG IDNot Available
Wikipedia LinkTrigonelline
METLIN ID273
PubChem Compound5570
PDB IDNot Available
ChEBI ID18123
Good Scents IDrw1698551
References
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. Pirpour Tazehkand A, Salehi R, Velaei K, Samadi N: The potential impact of trigonelline loaded micelles on Nrf2 suppression to overcome oxaliplatin resistance in colon cancer cells. Mol Biol Rep. 2020 Aug;47(8):5817-5829. doi: 10.1007/s11033-020-05650-w. Epub 2020 Jul 13. [PubMed:32661875 ]