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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:13:03 UTC

Update Date

2023-02-21 17:23:21 UTC

HMDB ID

HMDB0033485

Secondary Accession Numbers

HMDB33485

Metabolite Identification

Common Name

Gentiatibetine

Description

Gentiatibetine belongs to the class of organic compounds known as pyranopyridines. These are polycyclic aromatic compounds containing a pyran ring fused to a pyridine ring. Gentiatibetine has been detected, but not quantified in, a few different foods, such as alcoholic beverages, herbs and spices, and root vegetables. This could make gentiatibetine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Gentiatibetine.

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       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   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       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    4    7                                                       
CONECT    3    5    7                                                       
CONECT    4    2   10                                                       
CONECT    5    3   12                                                       
CONECT    6    1    8   10                                                  
CONECT    7    2    3    8                                                  
CONECT    8    6    7    9                                                  
CONECT    9    8   11   12                                                  
CONECT   10    4    6                                                       
CONECT   11    9                                                            
CONECT   12    5    9                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Gentiotibetine	HMDB

Chemical Formula

C₉H₁₁NO₂

Average Molecular Weight

165.1891

Monoisotopic Molecular Weight

165.078978601

IUPAC Name

8-methyl-1H,3H,4H-pyrano[3,4-c]pyridin-1-ol

Traditional Name

8-methyl-1H,3H,4H-pyrano[3,4-c]pyridin-1-ol

CAS Registry Number

26005-36-7

SMILES

CC1=C2C(O)OCCC2=CC=N1

InChI Identifier

InChI=1S/C9H11NO2/c1-6-8-7(2-4-10-6)3-5-12-9(8)11/h2,4,9,11H,3,5H2,1H3

InChI Key

HCBOYQSYWSEVID-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyranopyridines. These are polycyclic aromatic compounds containing a pyran ring fused to a pyridine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyranopyridines

Sub Class

Not Available

Direct Parent

Pyranopyridines

Alternative Parents

Substituents

Pyranopyridine
Methylpyridine
Pyridine
Heteroaromatic compound
Hemiacetal
Oxacycle
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
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: HMDB0033485)
Cytoplasm (HMDB: HMDB0033485)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033485)

Source

Exogenous

Food

Food (HMDB: HMDB0033485)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Root vegetable

Root vegetables (FooDB: FOOD00873)

Beverage

Alcoholic beverage

Alcoholic beverages (FooDB: FOOD00854)

Endogenous

Plant

Plant (HMDB: HMDB0033485)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033485)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	161.5 °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	111 g/L	ALOGPS
logP	0.34	ALOGPS
logP	0.44	ChemAxon
logS	-0.17	ALOGPS
pKa (Strongest Acidic)	11.44	ChemAxon
pKa (Strongest Basic)	5.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	42.35 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	44.4 m³·mol⁻¹	ChemAxon
Polarizability	17.14 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]+	137.348	31661259
DarkChem	[M-H]-	132.592	31661259
DeepCCS	[M+H]+	128.768	30932474
DeepCCS	[M-H]-	124.936	30932474
DeepCCS	[M-2H]-	162.028	30932474
DeepCCS	[M+Na]+	137.568	30932474
AllCCS	[M+H]+	134.4	32859911
AllCCS	[M+H-H2O]+	129.7	32859911
AllCCS	[M+NH4]+	138.7	32859911
AllCCS	[M+Na]+	139.9	32859911
AllCCS	[M-H]-	135.0	32859911
AllCCS	[M+Na-2H]-	135.8	32859911
AllCCS	[M+HCOO]-	136.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Gentiatibetine	CC1=C2C(O)OCCC2=CC=N1	2426.1	Standard polar	33892256
Gentiatibetine	CC1=C2C(O)OCCC2=CC=N1	1430.8	Standard non polar	33892256
Gentiatibetine	CC1=C2C(O)OCCC2=CC=N1	1544.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Gentiatibetine,1TMS,isomer #1	CC1=NC=CC2=C1C(O[Si](C)(C)C)OCC2	1526.9	Semi standard non polar	33892256
Gentiatibetine,1TBDMS,isomer #1	CC1=NC=CC2=C1C(O[Si](C)(C)C(C)(C)C)OCC2	1785.6	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 - Gentiatibetine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0673-2900000000-398e635127dd6f7f3f60	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gentiatibetine GC-MS (1 TMS) - 70eV, Positive	splash10-00di-9720000000-f0af6ef9f7231d878c57	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gentiatibetine 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 - Gentiatibetine 10V, Positive-QTOF	splash10-014i-0900000000-399b85f9980def424cb2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 20V, Positive-QTOF	splash10-014j-0900000000-29321b39ba369eb0e444	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 40V, Positive-QTOF	splash10-0ftf-9800000000-56fe68a119a43aefc4f1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 10V, Negative-QTOF	splash10-03di-0900000000-4cd3b4c03cf0f30a08db	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 20V, Negative-QTOF	splash10-03di-0900000000-3abf5ca3b897ea9991a8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 40V, Negative-QTOF	splash10-00kf-6900000000-8d87ec96e4558d4f6a29	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 10V, Positive-QTOF	splash10-014i-0900000000-a1ba3343ae0df78259df	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 20V, Positive-QTOF	splash10-00kb-0900000000-a69d5cb38d13c903b258	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 40V, Positive-QTOF	splash10-0l06-6900000000-b14de72780e7b7e03365	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 10V, Negative-QTOF	splash10-03di-0900000000-58730e09c186a15c21ca	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 20V, Negative-QTOF	splash10-03di-0900000000-f006727ca44dd81f6bed	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentiatibetine 40V, Negative-QTOF	splash10-0006-9700000000-49865bcad3fef98fa78d	2021-09-24	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

FDB011529

KNApSAcK ID

Not Available

Chemspider ID

4476406

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5317559

PDB ID

Not Available

ChEBI ID

173740

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 Gentiatibetine (HMDB0033485)

MOL for HMDB0033485 (Gentiatibetine)

3D MOL for HMDB0033485 (Gentiatibetine)

3D SDF for HMDB0033485 (Gentiatibetine)

3D-SDF for HMDB0033485 (Gentiatibetine)

PDB for HMDB0033485 (Gentiatibetine)

3D PDB for HMDB0033485 (Gentiatibetine)

SMILES for HMDB0033485 (Gentiatibetine)

INCHI for HMDB0033485 (Gentiatibetine)

Structure for HMDB0033485 (Gentiatibetine)

3D Structure for HMDB0033485 (Gentiatibetine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra