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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:33:10 UTC

Update Date

2023-02-21 17:19:20 UTC

HMDB ID

HMDB0029873

Secondary Accession Numbers

HMDB29873

Metabolite Identification

Common Name

(S)-Spinacine

Description

(S)-Spinacine, also known as spinacine, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Based on a literature review very few articles have been published on (S)-Spinacine.

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       1.770  -3.233   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.383  -2.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.077  -1.232   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -1.462  -0.769   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.770   0.769   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.693   1.692   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.693   3.232   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.846   3.848   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.770   2.463   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.846   1.231   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.154  -0.153   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.846  -3.848   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    6    9   11                                                  
CONECT   11    3   10                                                       
CONECT   12    2                                                            
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
Spinacine	HMDB
4,5,6,7-Tetrahydro-1H-imidazo(4,5-c)pyridine-6-carboxylic acid	HMDB
3H,4H,5H,6H,7H-Imidazo[4,5-c]pyridine-6-carboxylate	HMDB

Chemical Formula

C₇H₉N₃O₂

Average Molecular Weight

167.1653

Monoisotopic Molecular Weight

167.069476547

IUPAC Name

1H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-6-carboxylic acid

Traditional Name

1H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-6-carboxylic acid

CAS Registry Number

59981-63-4

SMILES

OC(=O)C1CC2=C(CN1)N=CN2

InChI Identifier

InChI=1S/C7H9N3O2/c11-7(12)5-1-4-6(2-8-5)10-3-9-4/h3,5,8H,1-2H2,(H,9,10)(H,11,12)

InChI Key

YCFJXOFFQLPCHD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Imidazopiperidine
Imidazopyridine
Aralkylamine
Azole
Imidazole
Heteroaromatic compound
Amino acid
Carboxylic acid
Secondary aliphatic amine
Azacycle
Organoheterocyclic compound
Secondary amine
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029873)
Cytoplasm (HMDB: HMDB0029873)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0029873)

Source

Endogenous

Endogenous (HMDB: HMDB0029873)

Plant

Plant (HMDB: HMDB0029873)

Animal

Animal (HMDB: HMDB0029873)

Exogenous

Food

Food (HMDB: HMDB0029873)

Tea

Vegetable

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

Beverage

Beverages (FooDB: FOOD00870)

Aquatic origin

Crustacean

Crustaceans (FooDB: FOOD00862)

Exogenous (HMDB: HMDB0029873)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	265 °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	6.2 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-3.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.31	ChemAxon
pKa (Strongest Basic)	8.08	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	78.01 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	40.87 m³·mol⁻¹	ChemAxon
Polarizability	16.16 Å³	ChemAxon
Number of Rings	2	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
DarkChem	[M+H]+	137.044	31661259
DarkChem	[M-H]-	130.276	31661259
DeepCCS	[M+H]+	133.149	30932474
DeepCCS	[M-H]-	130.38	30932474
DeepCCS	[M-2H]-	166.991	30932474
DeepCCS	[M+Na]+	142.311	30932474
AllCCS	[M+H]+	136.3	32859911
AllCCS	[M+H-H2O]+	131.8	32859911
AllCCS	[M+NH4]+	140.5	32859911
AllCCS	[M+Na]+	141.7	32859911
AllCCS	[M-H]-	133.6	32859911
AllCCS	[M+Na-2H]-	134.3	32859911
AllCCS	[M+HCOO]-	135.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Spinacine	OC(=O)C1CC2=C(CN1)N=CN2	3232.9	Standard polar	33892256
(S)-Spinacine	OC(=O)C1CC2=C(CN1)N=CN2	1752.0	Standard non polar	33892256
(S)-Spinacine	OC(=O)C1CC2=C(CN1)N=CN2	2113.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Spinacine,1TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC2=C(CN1)N=C[NH]2	1906.5	Semi standard non polar	33892256
(S)-Spinacine,1TMS,isomer #2	C[Si](C)(C)N1CC2=C(CC1C(=O)O)[NH]C=N2	1980.2	Semi standard non polar	33892256
(S)-Spinacine,1TMS,isomer #3	C[Si](C)(C)N1C=NC2=C1CC(C(=O)O)NC2	2043.4	Semi standard non polar	33892256
(S)-Spinacine,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC2=C(CN1)N=CN2[Si](C)(C)C	1988.7	Semi standard non polar	33892256
(S)-Spinacine,2TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC2=C(CN1)N=CN2[Si](C)(C)C	1821.1	Standard non polar	33892256
(S)-Spinacine,2TMS,isomer #2	C[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C)N=C[NH]2	1981.8	Semi standard non polar	33892256
(S)-Spinacine,2TMS,isomer #2	C[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C)N=C[NH]2	1910.5	Standard non polar	33892256
(S)-Spinacine,2TMS,isomer #3	C[Si](C)(C)N1CC2=C(CC1C(=O)O)N([Si](C)(C)C)C=N2	2030.4	Semi standard non polar	33892256
(S)-Spinacine,2TMS,isomer #3	C[Si](C)(C)N1CC2=C(CC1C(=O)O)N([Si](C)(C)C)C=N2	1970.1	Standard non polar	33892256
(S)-Spinacine,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C)N=CN2[Si](C)(C)C	2031.6	Semi standard non polar	33892256
(S)-Spinacine,3TMS,isomer #1	C[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C)N=CN2[Si](C)(C)C	2005.2	Standard non polar	33892256
(S)-Spinacine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1)N=C[NH]2	2171.2	Semi standard non polar	33892256
(S)-Spinacine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1CC2=C(CC1C(=O)O)[NH]C=N2	2254.4	Semi standard non polar	33892256
(S)-Spinacine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1C=NC2=C1CC(C(=O)O)NC2	2290.8	Semi standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1)N=CN2[Si](C)(C)C(C)(C)C	2475.1	Semi standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1)N=CN2[Si](C)(C)C(C)(C)C	2319.5	Standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C(C)(C)C)N=C[NH]2	2461.3	Semi standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C(C)(C)C)N=C[NH]2	2440.5	Standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CC2=C(CC1C(=O)O)N([Si](C)(C)C(C)(C)C)C=N2	2514.9	Semi standard non polar	33892256
(S)-Spinacine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N1CC2=C(CC1C(=O)O)N([Si](C)(C)C(C)(C)C)C=N2	2445.5	Standard non polar	33892256
(S)-Spinacine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	2703.8	Semi standard non polar	33892256
(S)-Spinacine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C1CC2=C(CN1[Si](C)(C)C(C)(C)C)N=CN2[Si](C)(C)C(C)(C)C	2714.8	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)-Spinacine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-4900000000-628ec2d56da1d8337c9c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Spinacine GC-MS (1 TMS) - 70eV, Positive	splash10-00dl-6930000000-fd0185e878b8b2203fec	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Spinacine 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)-Spinacine 10V, Positive-QTOF	splash10-014i-0900000000-462a5f786f22597f198d	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 20V, Positive-QTOF	splash10-00di-3900000000-035f377689fdb3290597	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 40V, Positive-QTOF	splash10-05aj-9300000000-63fd314bf3ff9df7f952	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 10V, Negative-QTOF	splash10-014i-0900000000-152a252f21b79cec9b83	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 20V, Negative-QTOF	splash10-00xr-0900000000-fb4a570fba03a7d02a46	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 40V, Negative-QTOF	splash10-05bf-9700000000-b2dd66b20cf921ed0fb9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 10V, Positive-QTOF	splash10-014i-0900000000-7420146361adc64761cf	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 20V, Positive-QTOF	splash10-00dj-6900000000-2b169979a7300f193821	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 40V, Positive-QTOF	splash10-0kcu-9100000000-e30266519292e6683441	2021-09-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 10V, Negative-QTOF	splash10-014i-2900000000-b9414553d16fc8787f88	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 20V, Negative-QTOF	splash10-00di-4900000000-69a270dc8f20879d59c5	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Spinacine 40V, Negative-QTOF	splash10-0006-9200000000-66988af688bff53180fd	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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

FDB001102

KNApSAcK ID

Not Available

Chemspider ID

323081

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

363935

PDB ID

Not Available

ChEBI ID

355044

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)-Spinacine (HMDB0029873)

MOL for HMDB0029873 ((S)-Spinacine)

3D MOL for HMDB0029873 ((S)-Spinacine)

3D SDF for HMDB0029873 ((S)-Spinacine)

3D-SDF for HMDB0029873 ((S)-Spinacine)

PDB for HMDB0029873 ((S)-Spinacine)

3D PDB for HMDB0029873 ((S)-Spinacine)

SMILES for HMDB0029873 ((S)-Spinacine)

INCHI for HMDB0029873 ((S)-Spinacine)

Structure for HMDB0029873 ((S)-Spinacine)

3D Structure for HMDB0029873 ((S)-Spinacine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra