Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:12:53 UTC

Update Date

2023-02-21 17:23:20 UTC

HMDB ID

HMDB0033482

Secondary Accession Numbers

HMDB33482

Metabolite Identification

Common Name

Plantagonine

Description

Plantagonine belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. Plantagonine has been detected, but not quantified in, fruits. This could make plantagonine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Plantagonine.

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       1.650   1.408   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924  -4.383   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       6.258  -5.153   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.590  -5.153   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    3    6                                                       
CONECT    3    2    7                                                       
CONECT    4    8   11                                                       
CONECT    5    9   11                                                       
CONECT    6    1    2    8                                                  
CONECT    7    3    8    9                                                  
CONECT    8    4    6    7                                                  
CONECT    9    5    7   10                                                  
CONECT   10    9   12   13                                                  
CONECT   11    4    5                                                       
CONECT   12   10                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
7-Methyl-5H,6H,7H-cyclopenta[c]pyridine-4-carboxylate	HMDB

Chemical Formula

C₁₀H₁₁NO₂

Average Molecular Weight

177.1998

Monoisotopic Molecular Weight

177.078978601

IUPAC Name

7-methyl-5H,6H,7H-cyclopenta[c]pyridine-4-carboxylic acid

Traditional Name

7-methyl-5H,6H,7H-cyclopenta[c]pyridine-4-carboxylic acid

CAS Registry Number

21857-97-6

SMILES

CC1CCC2=C1C=NC=C2C(O)=O

InChI Identifier

InChI=1S/C10H11NO2/c1-6-2-3-7-8(6)4-11-5-9(7)10(12)13/h4-6H,2-3H2,1H3,(H,12,13)

InChI Key

RLNQBGQGMYNOCX-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridinecarboxylic acids and derivatives

Direct Parent

Pyridinecarboxylic acids

Alternative Parents

Substituents

Pyridine carboxylic acid
Heteroaromatic compound
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033482)
Cytoplasm (HMDB: HMDB0033482)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033482)

Source

Exogenous

Exogenous (HMDB: HMDB0033482)

Food

Food (HMDB: HMDB0033482)

Fruit

Fruits (FooDB: FOOD00871)

Endogenous

Plant

Plant (HMDB: HMDB0033482)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033482)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	218 - 220 °C	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
Water Solubility	8.9 g/L	ALOGPS
logP	1.47	ALOGPS
logP	0.51	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	2.04	ChemAxon
pKa (Strongest Basic)	6.22	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	50.19 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	48.59 m³·mol⁻¹	ChemAxon
Polarizability	18.39 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	140.644	31661259
DarkChem	[M-H]-	136.529	31661259
DeepCCS	[M+H]+	134.052	30932474
DeepCCS	[M-H]-	130.223	30932474
DeepCCS	[M-2H]-	167.376	30932474
DeepCCS	[M+Na]+	142.916	30932474
AllCCS	[M+H]+	138.2	32859911
AllCCS	[M+H-H2O]+	133.8	32859911
AllCCS	[M+NH4]+	142.2	32859911
AllCCS	[M+Na]+	143.4	32859911
AllCCS	[M-H]-	139.5	32859911
AllCCS	[M+Na-2H]-	140.0	32859911
AllCCS	[M+HCOO]-	140.7	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.	3.86 minutes	32390414
Predicted by Siyang on May 30, 2022	10.2902 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.25 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	34.9 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1138.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	315.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	123.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	195.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	89.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	337.1 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	455.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	70.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	800.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	295.2 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	1131.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	243.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	251.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	387.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	209.0 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	93.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Plantagonine	CC1CCC2=C1C=NC=C2C(O)=O	2441.1	Standard polar	33892256
Plantagonine	CC1CCC2=C1C=NC=C2C(O)=O	1659.1	Standard non polar	33892256
Plantagonine	CC1CCC2=C1C=NC=C2C(O)=O	1706.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Plantagonine,1TMS,isomer #1	CC1CCC2=C(C(=O)O[Si](C)(C)C)C=NC=C21	1706.0	Semi standard non polar	33892256
Plantagonine,1TBDMS,isomer #1	CC1CCC2=C(C(=O)O[Si](C)(C)C(C)(C)C)C=NC=C21	1941.1	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 - Plantagonine GC-MS (Non-derivatized) - 70eV, Positive	splash10-08gi-1900000000-2368537ec750735487db	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Plantagonine GC-MS (1 TMS) - 70eV, Positive	splash10-00e9-9450000000-6841cb53b0d91f8f20f2	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Plantagonine 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 - Plantagonine 10V, Positive-QTOF	splash10-004i-0900000000-373efe61543c3d4abf21	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 20V, Positive-QTOF	splash10-01si-0900000000-bbf73b0a62f974d76bf5	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 40V, Positive-QTOF	splash10-0ue9-5900000000-d5f673df69d4e74f29ac	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 10V, Negative-QTOF	splash10-003r-0900000000-da37249733238d1708ec	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 20V, Negative-QTOF	splash10-001i-0900000000-265634d281e6b8f824bd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 40V, Negative-QTOF	splash10-00lr-1900000000-2cc70bdabd831571a1ad	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 10V, Negative-QTOF	splash10-004i-0900000000-9db632f3cd943f1b84e7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 20V, Negative-QTOF	splash10-001i-0900000000-c5b40290de13ee0367ed	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 40V, Negative-QTOF	splash10-014i-0900000000-661078c12fa9bc121175	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 10V, Positive-QTOF	splash10-03e9-0900000000-384db33f0989f0797034	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 20V, Positive-QTOF	splash10-03di-0900000000-6f9d869cd53d020b9d39	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plantagonine 40V, Positive-QTOF	splash10-0kyl-4900000000-053e8d5093ddd6fdd933	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	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+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

FDB011526

KNApSAcK ID

C00055202

Chemspider ID

35013610

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12300211

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

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

Showing metabocard for Plantagonine (HMDB0033482)

MOL for HMDB0033482 (Plantagonine)

3D MOL for HMDB0033482 (Plantagonine)

3D SDF for HMDB0033482 (Plantagonine)

3D-SDF for HMDB0033482 (Plantagonine)

PDB for HMDB0033482 (Plantagonine)

3D PDB for HMDB0033482 (Plantagonine)

SMILES for HMDB0033482 (Plantagonine)

INCHI for HMDB0033482 (Plantagonine)

Structure for HMDB0033482 (Plantagonine)

3D Structure for HMDB0033482 (Plantagonine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra