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

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 18:10:03 UTC

Update Date

2023-02-21 17:23:18 UTC

HMDB ID

HMDB0033433

Secondary Accession Numbers

HMDB33433

Metabolite Identification

Common Name

(S)-Homostachydrine

Description

(S)-Homostachydrine (also known as pipecolic acid betaine or homostachydrine) can be found in green coffee beans of Robusta and Arabica species (PMID: 27006213 ). (S)-Homostachydrine content is unaffected by coffee bean roasting treatment because of its remarkable heat stability. This makes it a good candidate marker for determining the content of Robusta and Arabica species in roasted coffee blends. (S)-Homostachydrine is also a potential marker of coffee consumption as it can be found in both human serum and human urine. It is also found in alfalfa seeds and leaves. More specifically, (S)-homostachydrine can be isolated from the seeds of Medicago sativa (alfalfa) as well as from Achillea millefolium (yarrow). (S)-Homostachydrine is also found in the fruits, seeds, and leaves of orange, lemon, and bergamot (PMID: 22208890 ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Homostachydrine	HMDB
Pipecolic acid betaine	HMDB
S-Homostachydrine	HMDB
(2S)-1,1-Dimethylpiperidin-1-ium-2-carboxylic acid	Generator

Chemical Formula

C₈H₁₅NO₂

Average Molecular Weight

157.2102

Monoisotopic Molecular Weight

157.110278729

IUPAC Name

(2S)-1,1-dimethylpiperidin-1-ium-2-carboxylate

Traditional Name

homostachydrine

CAS Registry Number

472-22-0

SMILES

C[N+]1(C)CCCC[C@H]1C([O-])=O

InChI Identifier

InChI=1S/C8H15NO2/c1-9(2)6-4-3-5-7(9)8(10)11/h7H,3-6H2,1-2H3/t7-/m0/s1

InChI Key

XULZWQRXYTVUTE-ZETCQYMHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Piperidinecarboxylic acid
Piperidine
Quaternary ammonium salt
Tetraalkylammonium salt
Carboxylic acid salt
Carboxylic acid
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Azacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Amine
Organic salt
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Pyrrolidine alkaloids (C08283 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0033433)
Cytoplasm (HMDB: HMDB0033433)

Excreta

Biofluid or Excreta

Feces (HMDB: HMDB0033433)
Urine (PMID: 32966057)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 32966057)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033433)

Source

Exogenous

Food

Food (HMDB: HMDB0033433)

Herb and spice

Herb

Alfalfa (FooDB: FOOD00286)

Herbs and Spices (FooDB: FOOD00866)

Cereal and cereal product

Cereal product

Whole grain cereal products (HMDB: HMDB0033433)

Pulse

Pulses (FooDB: FOOD00867)

Endogenous

Plant

Plant (HMDB: HMDB0033433)
Fabaceae (HMDB: HMDB0033433)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0033433)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	300 °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	0.14 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.4	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	2.39	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	40.13 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	64.71 m³·mol⁻¹	ChemAxon
Polarizability	16.92 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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
DeepCCS	[M+H]+	129.251	30932474
DeepCCS	[M-H]-	125.812	30932474
DeepCCS	[M-2H]-	162.842	30932474
DeepCCS	[M+Na]+	138.118	30932474
AllCCS	[M+H]+	131.3	32859911
AllCCS	[M+H-H2O]+	126.9	32859911
AllCCS	[M+NH4]+	135.3	32859911
AllCCS	[M+Na]+	136.5	32859911
AllCCS	[M-H]-	141.3	32859911
AllCCS	[M+Na-2H]-	142.5	32859911
AllCCS	[M+HCOO]-	144.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Homostachydrine	C[N+]1(C)CCCC[C@H]1C([O-])=O	1855.9	Standard polar	33892256
(S)-Homostachydrine	C[N+]1(C)CCCC[C@H]1C([O-])=O	1077.7	Standard non polar	33892256
(S)-Homostachydrine	C[N+]1(C)CCCC[C@H]1C([O-])=O	1199.8	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)-Homostachydrine GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fr-9400000000-687b9b09f0e9c65ca3a9	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Homostachydrine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Homostachydrine 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)-Homostachydrine 10V, Positive-QTOF	splash10-0a4i-0900000000-6d4634868b41a48837ea	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 20V, Positive-QTOF	splash10-0bt9-2900000000-886043a617d75e47c1c5	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 40V, Positive-QTOF	splash10-0596-9100000000-0617d15a8a0a14a1f151	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 10V, Negative-QTOF	splash10-0a4i-0900000000-391842ea1e278385a6f1	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 20V, Negative-QTOF	splash10-0a4i-0900000000-55f9328a9190c2232707	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 40V, Negative-QTOF	splash10-0ar0-9000000000-6605fc93bf304ad99e07	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 10V, Positive-QTOF	splash10-03di-0900000000-7b2fe40c81420a678777	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 20V, Positive-QTOF	splash10-03di-5900000000-231bcfa989f73c026f39	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 40V, Positive-QTOF	splash10-0a4i-9100000000-9e558dde2f341c252059	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 10V, Negative-QTOF	splash10-0a4i-0900000000-0f7129c598f6efd38657	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 20V, Negative-QTOF	splash10-0a4i-0900000000-0f7129c598f6efd38657	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Homostachydrine 40V, Negative-QTOF	splash10-052f-9600000000-5f2a3091897e5f0660cc	2021-09-24	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

Blood
Feces
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details

Associated Disorders and Diseases

Disease References

Colorectal cancer

Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

114500 (Colorectal cancer)

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

441447

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

Servillo L, Giovane A, Casale R, Cautela D, D'Onofrio N, Balestrieri ML, Castaldo D: Homostachydrine (pipecolic acid betaine) as authentication marker of roasted blends of Coffea arabica and Coffea canephora (Robusta) beans. Food Chem. 2016 Aug 15;205:52-7. doi: 10.1016/j.foodchem.2016.02.154. Epub 2016 Mar 3. [PubMed:27006213 ]
Servillo L, Giovane A, Balestrieri ML, Ferrari G, Cautela D, Castaldo D: Occurrence of pipecolic acid and pipecolic acid betaine (homostachydrine) in Citrus genus plants. J Agric Food Chem. 2012 Jan 11;60(1):315-21. doi: 10.1021/jf204286r. Epub 2011 Dec 29. [PubMed:22208890 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for (S)-Homostachydrine (HMDB0033433)

MOL for HMDB0033433 ((S)-Homostachydrine)

3D MOL for HMDB0033433 ((S)-Homostachydrine)

3D SDF for HMDB0033433 ((S)-Homostachydrine)

3D-SDF for HMDB0033433 ((S)-Homostachydrine)

PDB for HMDB0033433 ((S)-Homostachydrine)

3D PDB for HMDB0033433 ((S)-Homostachydrine)

SMILES for HMDB0033433 ((S)-Homostachydrine)

INCHI for HMDB0033433 ((S)-Homostachydrine)

Structure for HMDB0033433 ((S)-Homostachydrine)

3D Structure for HMDB0033433 ((S)-Homostachydrine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra