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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:30:31 UTC

Update Date

2023-02-21 17:18:47 UTC

HMDB ID

HMDB0029455

Secondary Accession Numbers

HMDB29455

Metabolite Identification

Common Name

Ginkgotoxin

Description

Ginkgotoxin belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group. Based on a literature review a significant number of articles have been published on Ginkgotoxin.

Structure

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

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       1.347   2.993   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.347   1.496   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.001   0.748   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.347   1.496   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.544   0.748   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.544  -0.748   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.891  -1.496   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.891  -1.646   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.694  -0.897   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.347  -1.496   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.001  -0.748   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.347  -1.496   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.347  -2.993   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6                                                            
CONECT    8    9                                                            
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11    3   10   12                                                  
CONECT   12    6   11   13                                                  
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Hydroxy-5-hydroxymethyl-4-methoxymethyl-2-methylpyridine	HMDB
4'-Methoxypyridoxine	HMDB
4-Methoxymethylpyridoxine	HMDB
4-Methoxypyridoxine	HMDB
4-O-Methoxypyridoxine	HMDB
5-Hydroxy-4-(methoxymethyl)-6-methyl-3-pyridinemethanol	HMDB
5-Hydroxy-4-(methoxymethyl)-6-methyl-3-pyridinemethanol, 9ci	HMDB
4-Methoxymethylpyridoxine hydrochloride	HMDB
4-O-Methylpyridoxine	HMDB

Chemical Formula

C₉H₁₃NO₃

Average Molecular Weight

183.2044

Monoisotopic Molecular Weight

183.089543287

IUPAC Name

5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol

Traditional Name

ginkgotoxin

CAS Registry Number

1464-33-1

SMILES

COCC1=C(CO)C=NC(C)=C1O

InChI Identifier

InChI=1S/C9H13NO3/c1-6-9(12)8(5-13-2)7(4-11)3-10-6/h3,11-12H,4-5H2,1-2H3

InChI Key

SVINQHQHARVZFF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxines. These are pyridoxal derivatives in which the carbaldehyde group at position 2 of the pyridoxal moiety is replaced by a hydroxymethyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridoxines

Direct Parent

Pyridoxines

Alternative Parents

Substituents

Pyridoxine
Methylpyridine
Hydroxypyridine
Heteroaromatic compound
Dialkyl ether
Ether
Azacycle
Alcohol
Hydrocarbon derivative
Aromatic alcohol
Organopnictogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen 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: HMDB0029455)
Cytoplasm (HMDB: HMDB0029455)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029455)

Source

Endogenous

Endogenous (HMDB: HMDB0029455)

Exogenous

Food

Food (HMDB: HMDB0029455)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Exogenous (HMDB: HMDB0029455)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	181 °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	13.5 g/L	ALOGPS
logP	-0.08	ALOGPS
logP	-0.31	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	8.59	ChemAxon
pKa (Strongest Basic)	5.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	62.58 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	48.86 m³·mol⁻¹	ChemAxon
Polarizability	19.18 Å³	ChemAxon
Number of Rings	1	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]+	140.632	31661259
DarkChem	[M-H]-	138.431	31661259
DeepCCS	[M+H]+	145.387	30932474
DeepCCS	[M-H]-	142.409	30932474
DeepCCS	[M-2H]-	179.026	30932474
DeepCCS	[M+Na]+	154.437	30932474
AllCCS	[M+H]+	139.5	32859911
AllCCS	[M+H-H2O]+	135.3	32859911
AllCCS	[M+NH4]+	143.5	32859911
AllCCS	[M+Na]+	144.6	32859911
AllCCS	[M-H]-	139.5	32859911
AllCCS	[M+Na-2H]-	140.5	32859911
AllCCS	[M+HCOO]-	141.7	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.	2.37 minutes	32390414
Predicted by Siyang on May 30, 2022	9.452 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	58.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	513.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	263.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	97.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	155.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	41.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	245.7 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	306.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	356.8 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	651.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	45.7 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	910.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.0 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	204.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	412.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	404.8 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	295.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ginkgotoxin	COCC1=C(CO)C=NC(C)=C1O	2526.2	Standard polar	33892256
Ginkgotoxin	COCC1=C(CO)C=NC(C)=C1O	1606.9	Standard non polar	33892256
Ginkgotoxin	COCC1=C(CO)C=NC(C)=C1O	1650.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ginkgotoxin,1TMS,isomer #1	COCC1=C(CO[Si](C)(C)C)C=NC(C)=C1O	1685.1	Semi standard non polar	33892256
Ginkgotoxin,1TMS,isomer #2	COCC1=C(CO)C=NC(C)=C1O[Si](C)(C)C	1657.5	Semi standard non polar	33892256
Ginkgotoxin,2TMS,isomer #1	COCC1=C(CO[Si](C)(C)C)C=NC(C)=C1O[Si](C)(C)C	1739.8	Semi standard non polar	33892256
Ginkgotoxin,1TBDMS,isomer #1	COCC1=C(CO[Si](C)(C)C(C)(C)C)C=NC(C)=C1O	1906.0	Semi standard non polar	33892256
Ginkgotoxin,1TBDMS,isomer #2	COCC1=C(CO)C=NC(C)=C1O[Si](C)(C)C(C)(C)C	1913.5	Semi standard non polar	33892256
Ginkgotoxin,2TBDMS,isomer #1	COCC1=C(CO[Si](C)(C)C(C)(C)C)C=NC(C)=C1O[Si](C)(C)C(C)(C)C	2188.7	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 - Ginkgotoxin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udi-0900000000-509e318784475a90c6ae	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgotoxin GC-MS (2 TMS) - 70eV, Positive	splash10-03mi-7094000000-06bcae9305956458f788	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgotoxin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginkgotoxin 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 - Ginkgotoxin 10V, Positive-QTOF	splash10-00lr-0900000000-d03869cbfe0de48f957f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 20V, Positive-QTOF	splash10-0159-0900000000-f7dcf2edcd0ec3acadc9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 40V, Positive-QTOF	splash10-001r-5900000000-62612c619376d008af1d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 10V, Negative-QTOF	splash10-001i-0900000000-d3ed817911f71b68623b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 20V, Negative-QTOF	splash10-0ul0-0900000000-fd233da20ebe5266b5b3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 40V, Negative-QTOF	splash10-0a4i-9400000000-8f59d8b20fe1e4bb8935	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 10V, Negative-QTOF	splash10-0a5i-0900000000-fcded58da1c48ed09818	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 20V, Negative-QTOF	splash10-0a4i-0900000000-cea0b2995b3de999a031	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 40V, Negative-QTOF	splash10-0ab9-2900000000-9a853490ae1ad6129bdc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 10V, Positive-QTOF	splash10-0f89-0900000000-c927fa0b991967577c60	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 20V, Positive-QTOF	splash10-0f89-0900000000-f511bd27a6eac4f4dad8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginkgotoxin 40V, Positive-QTOF	splash10-0080-3900000000-b0acc95302f9e5bcaf34	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)	2021-09-25	Wishart Lab	View Spectrum
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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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, 900 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

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	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

FDB000576

KNApSAcK ID

C00047902

Chemspider ID

69046

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Ginkgotoxin

METLIN ID

Not Available

PubChem Compound

76581

PDB ID

GT0

ChEBI ID

714289

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 Ginkgotoxin (HMDB0029455)

MOL for HMDB0029455 (Ginkgotoxin)

3D MOL for HMDB0029455 (Ginkgotoxin)

3D SDF for HMDB0029455 (Ginkgotoxin)

3D-SDF for HMDB0029455 (Ginkgotoxin)

PDB for HMDB0029455 (Ginkgotoxin)

3D PDB for HMDB0029455 (Ginkgotoxin)

SMILES for HMDB0029455 (Ginkgotoxin)

INCHI for HMDB0029455 (Ginkgotoxin)

Structure for HMDB0029455 (Ginkgotoxin)

3D Structure for HMDB0029455 (Ginkgotoxin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra