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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:36:16 UTC

Update Date

2023-02-21 17:19:32 UTC

HMDB ID

HMDB0030346

Secondary Accession Numbers

HMDB30346

Metabolite Identification

Common Name

(S)-Actinidine

Description

(S)-Actinidine belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group (S)-Actinidine has been detected, but not quantified in, several different foods, such as black tea, kiwis (Actinidia chinensis), fruits, teas (Camellia sinensis), and herbal tea. This could make (S)-actinidine a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on (S)-Actinidine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(7S)-4,7-Dimethyl-6,7-dihydro-5H-cyclopenta[c]pyridine	HMDB
6,7-dihydro-4,7-Dimethyl-(S)-5H-2-pyrindine	HMDB
Actinidine	HMDB
Actinidine hydrochloride, (+)-(R)-isomer	MeSH, HMDB

Chemical Formula

C₁₀H₁₃N

Average Molecular Weight

147.2169

Monoisotopic Molecular Weight

147.104799421

IUPAC Name

4,7-dimethyl-5H,6H,7H-cyclopenta[c]pyridine

Traditional Name

4,7-dimethyl-5H,6H,7H-cyclopenta[c]pyridine

CAS Registry Number

524-03-8

SMILES

CC1CCC2=C(C)C=NC=C12

InChI Identifier

InChI=1S/C10H13N/c1-7-3-4-9-8(2)5-11-6-10(7)9/h5-7H,3-4H2,1-2H3

InChI Key

ZHQQRIUYLMXDPP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methylpyridines. These are organic compounds containing a pyridine ring substituted at one or more positions by a methyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Methylpyridines

Direct Parent

Methylpyridines

Alternative Parents

Substituents

Methylpyridine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0030346)
Cell membrane (HMDB: HMDB0030346)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030346)

Source

Endogenous

Endogenous (HMDB: HMDB0030346)

Plant

Plant (HMDB: HMDB0030346)

Exogenous

Food

Food (HMDB: HMDB0030346)

Fruit

Tropical fruit

Kiwi (FooDB: FOOD00004)

Fruits (FooDB: FOOD00871)

Tea

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Exogenous (HMDB: HMDB0030346)

Not Available

EC 3.1.1.8 (cholinesterase) inhibitor (HMDB: HMDB0030346)

Industrial application

Agriculture

Pesticide

Fungicide (HMDB: HMDB0030346)

Pesticide (HMDB: HMDB0030346)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	223.23 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	2648 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	2.635 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.53 g/L	ALOGPS
logP	2.85	ALOGPS
logP	2.56	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Basic)	6.58	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	12.89 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	46.37 m³·mol⁻¹	ChemAxon
Polarizability	17.35 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	132.599	31661259
DarkChem	[M-H]-	129.316	31661259
DeepCCS	[M-2H]-	169.133	30932474
DeepCCS	[M+Na]+	144.514	30932474
AllCCS	[M+H]+	129.5	32859911
AllCCS	[M+H-H2O]+	124.8	32859911
AllCCS	[M+NH4]+	133.9	32859911
AllCCS	[M+Na]+	135.2	32859911
AllCCS	[M-H]-	134.4	32859911
AllCCS	[M+Na-2H]-	135.4	32859911
AllCCS	[M+HCOO]-	136.7	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.	3.98 minutes	32390414
Predicted by Siyang on May 30, 2022	11.416 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.98 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	25.7 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1208.7 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	353.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	145.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	217.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	97.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	399.2 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	476.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	83.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	963.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	313.8 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	1140.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	287.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	271.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	368.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	292.0 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	51.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Actinidine	CC1CCC2=C(C)C=NC=C12	1714.8	Standard polar	33892256
(S)-Actinidine	CC1CCC2=C(C)C=NC=C12	1282.1	Standard non polar	33892256
(S)-Actinidine	CC1CCC2=C(C)C=NC=C12	1296.6	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 - (S)-Actinidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00ls-0900000000-9dd6cee51fead7563c9b	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Actinidine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Actinidine 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)-Actinidine 10V, Positive-QTOF	splash10-0002-0900000000-96c0eac3aa6e0b53eda4	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 20V, Positive-QTOF	splash10-0002-0900000000-abaea544aa4e0d3863f3	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 40V, Positive-QTOF	splash10-0zfu-9500000000-e707ec14de56ef0beb78	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 10V, Negative-QTOF	splash10-0002-0900000000-83cd258222581160ab1b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 20V, Negative-QTOF	splash10-0002-0900000000-585b50f9ce09006b3f7f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 40V, Negative-QTOF	splash10-00ls-2900000000-d8c39ab190dc281d7a35	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 10V, Negative-QTOF	splash10-0002-0900000000-275b1c91e27cb2fd9267	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 20V, Negative-QTOF	splash10-0002-0900000000-275b1c91e27cb2fd9267	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 40V, Negative-QTOF	splash10-0006-0900000000-07f259413e7871b54796	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 10V, Positive-QTOF	splash10-0002-0900000000-914f577946648e5d4124	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 20V, Positive-QTOF	splash10-0002-2900000000-49c8435e2adf3a7ea17e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Actinidine 40V, Positive-QTOF	splash10-000x-9600000000-262b8f64323189fae902	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	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+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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

3530562

PDB ID

Not Available

ChEBI ID

2443

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1603911

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)-Actinidine (HMDB0030346)

MOL for HMDB0030346 ((S)-Actinidine)

3D MOL for HMDB0030346 ((S)-Actinidine)

3D SDF for HMDB0030346 ((S)-Actinidine)

3D-SDF for HMDB0030346 ((S)-Actinidine)

PDB for HMDB0030346 ((S)-Actinidine)

3D PDB for HMDB0030346 ((S)-Actinidine)

SMILES for HMDB0030346 ((S)-Actinidine)

INCHI for HMDB0030346 ((S)-Actinidine)

Structure for HMDB0030346 ((S)-Actinidine)

3D Structure for HMDB0030346 ((S)-Actinidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra