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

2017-03-23 04:54:37 UTC

Update Date

2022-03-07 03:17:57 UTC

HMDB ID

HMDB0062634

Secondary Accession Numbers

HMDB62634

Metabolite Identification

Common Name

(S)-carnitinium

Description

(S)-carnitinium belongs to the class of organic compounds known as carnitines. These are organic compounds containing the quaternary ammonium compound carnitine (S)-carnitinium is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

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

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    8                                                            
CONECT    4    6    7                                                       
CONECT    5    6    8                                                       
CONECT    6    4    5    9   12                                             
CONECT    7    4   10   11                                                  
CONECT    8    1    2    3    5                                             
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

COMPND    HMDB0062634
HETATM    1  C1  UNL     1      -1.926   0.785  -0.804  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.341  -0.031   0.215  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -1.229   0.783   1.418  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.225  -1.144   0.490  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.047  -0.576  -0.144  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.816   0.386  -0.875  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.055   1.521  -0.069  1.00  0.00           O  
HETATM    8  C6  UNL     1       2.128  -0.241  -1.240  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.936  -0.693  -0.109  1.00  0.00           C  
HETATM   10  O2  UNL     1       4.000  -1.327  -0.347  1.00  0.00           O  
HETATM   11  O3  UNL     1       2.613  -0.470   1.205  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.817   0.325  -1.806  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.515   1.814  -0.789  1.00  0.00           H  
HETATM   14  H3  UNL     1      -3.015   0.891  -0.553  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.511   1.830   1.261  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.177   0.766   1.763  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.847   0.351   2.250  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.685  -2.117   0.484  1.00  0.00           H  
HETATM   19  H8  UNL     1      -3.022  -1.244  -0.286  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.719  -1.006   1.483  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.195  -1.480  -0.781  1.00  0.00           H  
HETATM   22  H11 UNL     1       0.427  -0.900   0.787  1.00  0.00           H  
HETATM   23  H12 UNL     1       0.364   0.749  -1.826  1.00  0.00           H  
HETATM   24  H13 UNL     1       1.998   1.540   0.201  1.00  0.00           H  
HETATM   25  H14 UNL     1       1.983  -1.090  -1.975  1.00  0.00           H  
HETATM   26  H15 UNL     1       2.756   0.518  -1.789  1.00  0.00           H  
HETATM   27  H16 UNL     1       3.194   0.059   1.837  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    5
CONECT    3   15   16   17
CONECT    4   18   19   20
CONECT    5    6   21   22
CONECT    6    7    8   23
CONECT    7   24
CONECT    8    9   25   26
CONECT    9   10   10   11
CONECT   11   27
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₇H₁₆NO₃

Average Molecular Weight

162.2068

Monoisotopic Molecular Weight

162.113018383

IUPAC Name

[(2S)-3-carboxy-2-hydroxypropyl]trimethylazanium

Traditional Name

(S)-carnitinium

CAS Registry Number

Not Available

SMILES

[H][C@](O)(CC(O)=O)C[N+](C)(C)C

InChI Identifier

InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/p+1/t6-/m0/s1

InChI Key

PHIQHXFUZVPYII-LURJTMIESA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as carnitines. These are organic compounds containing the quaternary ammonium compound carnitine.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Quaternary ammonium salts

Direct Parent

Carnitines

Alternative Parents

Substituents

Carnitine
Beta-hydroxy acid
Short-chain hydroxy acid
Fatty acid
Hydroxy acid
Tetraalkylammonium salt
1,2-aminoalcohol
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxygen compound
Alcohol
Organooxygen compound
Organic salt
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Amine
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carnitinium (CHEBI:51453 )

Ontology

Not Available

Exogenous (HMDB: HMDB0062634)

Process

Not Available

Role

Not Available

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	6.58 g/l	ALOGPS
LogP	-2.75	ALOGPS

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.8	ALOGPS
logP	-4.9	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	4.2	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	52.65 m³·mol⁻¹	ChemAxon
Polarizability	17.2 Å³	ChemAxon
Number of Rings	0	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]+	135.733	31661259
DarkChem	[M-H]-	132.404	31661259
DeepCCS	[M+H]+	143.881	30932474
DeepCCS	[M-H]-	141.957	30932474
DeepCCS	[M-2H]-	175.336	30932474
DeepCCS	[M+Na]+	149.794	30932474
AllCCS	[M+H]+	135.1	32859911
AllCCS	[M+H-H2O]+	131.4	32859911
AllCCS	[M+NH4]+	138.5	32859911
AllCCS	[M+Na]+	139.5	32859911
AllCCS	[M-H]-	145.0	32859911
AllCCS	[M+Na-2H]-	146.8	32859911
AllCCS	[M+HCOO]-	148.8	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.	0.93 minutes	32390414
Predicted by Siyang on May 30, 2022	8.611 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.25 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	374.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	250.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	74.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	165.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	42.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	251.7 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	242.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	852.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	597.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	41.3 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	882.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	192.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	738.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	526.5 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	183.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-carnitinium	[H][C@](O)(CC(O)=O)C[N+](C)(C)C	2369.4	Standard polar	33892256
(S)-carnitinium	[H][C@](O)(CC(O)=O)C[N+](C)(C)C	1123.9	Standard non polar	33892256
(S)-carnitinium	[H][C@](O)(CC(O)=O)C[N+](C)(C)C	1323.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-carnitinium,1TMS,isomer #1	C[N+](C)(C)C[C@H](CC(=O)O)O[Si](C)(C)C	1343.9	Semi standard non polar	33892256
(S)-carnitinium,1TMS,isomer #2	C[N+](C)(C)C[C@@H](O)CC(=O)O[Si](C)(C)C	1329.7	Semi standard non polar	33892256
(S)-carnitinium,2TMS,isomer #1	C[N+](C)(C)C[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C	1400.1	Semi standard non polar	33892256
(S)-carnitinium,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@@H](CC(=O)O)C[N+](C)(C)C	1552.4	Semi standard non polar	33892256
(S)-carnitinium,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O)C[N+](C)(C)C	1551.2	Semi standard non polar	33892256
(S)-carnitinium,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](C[N+](C)(C)C)O[Si](C)(C)C(C)(C)C	1848.3	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)-carnitinium GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-9100000000-536725da5722f21418a0	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-carnitinium GC-MS (2 TMS) - 70eV, Positive	splash10-00dr-9130000000-455108a3e54a9eb18829	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-carnitinium 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)-carnitinium 10V, Positive-QTOF	splash10-01ox-0900000000-fe7021da394a24880212	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-carnitinium 20V, Positive-QTOF	splash10-02bf-1900000000-a655a8313901692115f6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-carnitinium 40V, Positive-QTOF	splash10-00di-9200000000-3d86c3fcd4004bf677b5	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-carnitinium 10V, Positive-QTOF	splash10-03di-5900000000-b811d656ee8c40cbce4a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-carnitinium 20V, Positive-QTOF	splash10-01p9-9200000000-664d5c24fd8a78a75d53	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-carnitinium 40V, Positive-QTOF	splash10-0bt9-9000000000-373e172dffad6b4c9d2c	2021-09-23	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

Biological Properties

Cellular Locations

Not Available

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

160907

PDB ID

DCK

ChEBI ID

51453

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

Not Available

Showing metabocard for (S)-carnitinium (HMDB0062634)

MOL for HMDB0062634 ((S)-carnitinium)

3D MOL for HMDB0062634 ((S)-carnitinium)

3D SDF for HMDB0062634 ((S)-carnitinium)

3D-SDF for HMDB0062634 ((S)-carnitinium)

PDB for HMDB0062634 ((S)-carnitinium)

3D PDB for HMDB0062634 ((S)-carnitinium)

SMILES for HMDB0062634 ((S)-carnitinium)

INCHI for HMDB0062634 ((S)-carnitinium)

Structure for HMDB0062634 ((S)-carnitinium)

3D Structure for HMDB0062634 ((S)-carnitinium)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra