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 18:13:00 UTC

Update Date

2023-02-21 17:23:20 UTC

HMDB ID

HMDB0033484

Secondary Accession Numbers

HMDB33484

Metabolite Identification

Common Name

(S)-Valerianine

Description

(S)-Valerianine belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms (S)-Valerianine has been detected, but not quantified in, several different foods, such as black tea, fats and oils, red tea, teas (Camellia sinensis), and green tea. This could make (S)-valerianine a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on (S)-Valerianine.

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       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       7.454   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2   13                                                            
CONECT    3    4    8                                                       
CONECT    4    3   10                                                       
CONECT    5    9   12                                                       
CONECT    6   11   12                                                       
CONECT    7    9   13                                                       
CONECT    8    1    3   11                                                  
CONECT    9    5    7   10                                                  
CONECT   10    4    9   11                                                  
CONECT   11    6    8   10                                                  
CONECT   12    5    6                                                       
CONECT   13    2    7                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

COMPND    HMDB0033484
HETATM    1  C1  UNL     1       3.758  -1.235   0.980  1.00  0.00           C  
HETATM    2  O1  UNL     1       2.455  -0.716   0.929  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.412   0.097  -0.211  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.101   0.783  -0.332  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.115   2.151  -0.550  1.00  0.00           C  
HETATM    6  N1  UNL     1      -0.042   2.838  -0.707  1.00  0.00           N  
HETATM    7  C5  UNL     1      -1.192   2.120  -0.646  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.229   0.769  -0.437  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.058   0.049  -0.270  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.324  -1.365  -0.014  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.829  -1.431   0.297  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.388  -0.189  -0.327  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.528   0.398   0.442  1.00  0.00           C  
HETATM   14  H1  UNL     1       3.840  -1.968   1.845  1.00  0.00           H  
HETATM   15  H2  UNL     1       4.154  -1.647   0.050  1.00  0.00           H  
HETATM   16  H3  UNL     1       4.451  -0.380   1.353  1.00  0.00           H  
HETATM   17  H4  UNL     1       2.659  -0.466  -1.115  1.00  0.00           H  
HETATM   18  H5  UNL     1       3.201   0.874  -0.089  1.00  0.00           H  
HETATM   19  H6  UNL     1       2.090   2.658  -0.612  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.087   2.723  -0.767  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.159  -1.994  -0.883  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.176  -1.773   0.919  1.00  0.00           H  
HETATM   23  H10 UNL     1      -2.031  -1.408   1.367  1.00  0.00           H  
HETATM   24  H11 UNL     1      -2.316  -2.316  -0.128  1.00  0.00           H  
HETATM   25  H12 UNL     1      -2.733  -0.427  -1.345  1.00  0.00           H  
HETATM   26  H13 UNL     1      -4.516  -0.034   0.164  1.00  0.00           H  
HETATM   27  H14 UNL     1      -3.391   0.398   1.542  1.00  0.00           H  
HETATM   28  H15 UNL     1      -3.587   1.490   0.147  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3
CONECT    3    4   17   18
CONECT    4    5    5    9
CONECT    5    6   19
CONECT    6    7    7
CONECT    7    8   20
CONECT    8    9    9   12
CONECT    9   10
CONECT   10   11   21   22
CONECT   11   12   23   24
CONECT   12   13   25
CONECT   13   26   27   28
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Valerianine	HMDB

Chemical Formula

C₁₁H₁₅NO

Average Molecular Weight

177.2429

Monoisotopic Molecular Weight

177.115364107

IUPAC Name

4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridine

Traditional Name

4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridine

CAS Registry Number

30634-66-3

SMILES

COCC1=C2CCC(C)C2=CN=C1

InChI Identifier

InChI=1S/C11H15NO/c1-8-3-4-10-9(7-13-2)5-12-6-11(8)10/h5-6,8H,3-4,7H2,1-2H3

InChI Key

ZRJLCVQCZVXUFB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Not Available

Direct Parent

Pyridines and derivatives

Alternative Parents

Substituents

Pyridine
Heteroaromatic compound
Azacycle
Ether
Dialkyl ether
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: HMDB0033484)
Cytoplasm (HMDB: HMDB0033484)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033484)

Source

Exogenous

Exogenous (HMDB: HMDB0033484)

Food

Food (HMDB: HMDB0033484)

Tea

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Endogenous

Plant

Plant (HMDB: HMDB0033484)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033484)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	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	3.1 g/L	ALOGPS
logP	1.96	ALOGPS
logP	1.93	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Basic)	5.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	22.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.9 m³·mol⁻¹	ChemAxon
Polarizability	20.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	140.02	31661259
DarkChem	[M-H]-	138.213	31661259
DeepCCS	[M+H]+	142.758	30932474
DeepCCS	[M-H]-	138.93	30932474
DeepCCS	[M-2H]-	176.512	30932474
DeepCCS	[M+Na]+	152.05	30932474
AllCCS	[M+H]+	138.9	32859911
AllCCS	[M+H-H2O]+	134.5	32859911
AllCCS	[M+NH4]+	142.9	32859911
AllCCS	[M+Na]+	144.1	32859911
AllCCS	[M-H]-	143.9	32859911
AllCCS	[M+Na-2H]-	144.6	32859911
AllCCS	[M+HCOO]-	145.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Valerianine	COCC1=C2CCC(C)C2=CN=C1	1995.4	Standard polar	33892256
(S)-Valerianine	COCC1=C2CCC(C)C2=CN=C1	1425.9	Standard non polar	33892256
(S)-Valerianine	COCC1=C2CCC(C)C2=CN=C1	1505.9	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 - (S)-Valerianine GC-MS (Non-derivatized) - 70eV, Positive	splash10-01ot-1900000000-b2b99c2cd86f18ea9976	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Valerianine 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 - (S)-Valerianine 10V, Positive-QTOF	splash10-004i-0900000000-1c91c43c03ed3cf5a0cb	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 20V, Positive-QTOF	splash10-004j-0900000000-189811ab9c50d20607c5	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 40V, Positive-QTOF	splash10-0159-3900000000-717a23bec8e9a5c4ff51	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 10V, Negative-QTOF	splash10-004i-0900000000-2df73a0c9aec7a0bac9f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 20V, Negative-QTOF	splash10-004i-0900000000-d39e9357bf35b874610b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 40V, Negative-QTOF	splash10-01q9-3900000000-78b20bb5854ec27bcacb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 10V, Positive-QTOF	splash10-005a-0900000000-a5da5ccc4f14fef45233	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 20V, Positive-QTOF	splash10-0002-0900000000-247336e03c068719d2da	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 40V, Positive-QTOF	splash10-053s-1900000000-d617fa5139772f1cdb9d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 10V, Negative-QTOF	splash10-003r-0900000000-08eafc42a63f84645d52	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 20V, Negative-QTOF	splash10-001i-0900000000-addeefdfa1bc56f390e5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Valerianine 40V, Negative-QTOF	splash10-00lr-0900000000-5754bc1874976a36f58d	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]+)	2023-02-04	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

182008

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 (S)-Valerianine (HMDB0033484)

MOL for HMDB0033484 ((S)-Valerianine)

3D MOL for HMDB0033484 ((S)-Valerianine)

3D SDF for HMDB0033484 ((S)-Valerianine)

3D-SDF for HMDB0033484 ((S)-Valerianine)

PDB for HMDB0033484 ((S)-Valerianine)

3D PDB for HMDB0033484 ((S)-Valerianine)

SMILES for HMDB0033484 ((S)-Valerianine)

INCHI for HMDB0033484 ((S)-Valerianine)

Structure for HMDB0033484 ((S)-Valerianine)

3D Structure for HMDB0033484 ((S)-Valerianine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra