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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:36:32 UTC

Update Date

2023-02-21 17:19:35 UTC

HMDB ID

HMDB0030393

Secondary Accession Numbers

HMDB30393

Metabolite Identification

Common Name

L-N-Carboxymethylserine

Description

L-N-Carboxymethylserine belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on L-N-Carboxymethylserine.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
N-Carboxymethyl-L-serine	HMDB
2-[(Carboxymethyl)amino]-3-hydroxypropanoate	HMDB

Chemical Formula

C₅H₉NO₅

Average Molecular Weight

163.1287

Monoisotopic Molecular Weight

163.048072403

IUPAC Name

2-[(carboxymethyl)amino]-3-hydroxypropanoic acid

Traditional Name

2-[(carboxymethyl)amino]-3-hydroxypropanoic acid

CAS Registry Number

17136-47-9

SMILES

OCC(NCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C5H9NO5/c7-2-3(5(10)11)6-1-4(8)9/h3,6-7H,1-2H2,(H,8,9)(H,10,11)

InChI Key

NAALTSITEQTADZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Serine and derivatives

Alternative Parents

Substituents

Serine or derivatives
Alpha-amino acid
Beta-hydroxy acid
Dicarboxylic acid or derivatives
Hydroxy acid
Amino acid
Carboxylic acid
Secondary aliphatic amine
Secondary amine
Alcohol
Organooxygen compound
Organonitrogen compound
Primary alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Amine
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0030393)
Cytoplasm (HMDB: HMDB0030393)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030393)

Source

Endogenous

Endogenous (HMDB: HMDB0030393)

Plant

Plant (HMDB: HMDB0030393)

Exogenous

Food

Food (HMDB: HMDB0030393)

Vegetable

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

Exogenous (HMDB: HMDB0030393)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	167 °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	60.4 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4.5	ChemAxon
logS	-0.43	ALOGPS
pKa (Strongest Acidic)	2.18	ChemAxon
pKa (Strongest Basic)	8.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	106.86 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	32.9 m³·mol⁻¹	ChemAxon
Polarizability	14.37 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]+	136.967	31661259
DarkChem	[M-H]-	133.343	31661259
DeepCCS	[M+H]+	129.24	30932474
DeepCCS	[M-H]-	126.042	30932474
DeepCCS	[M-2H]-	163.0	30932474
DeepCCS	[M+Na]+	137.885	30932474
AllCCS	[M+H]+	136.3	32859911
AllCCS	[M+H-H2O]+	132.4	32859911
AllCCS	[M+NH4]+	139.9	32859911
AllCCS	[M+Na]+	140.9	32859911
AllCCS	[M-H]-	128.9	32859911
AllCCS	[M+Na-2H]-	130.8	32859911
AllCCS	[M+HCOO]-	132.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
L-N-Carboxymethylserine	OCC(NCC(O)=O)C(O)=O	2693.0	Standard polar	33892256
L-N-Carboxymethylserine	OCC(NCC(O)=O)C(O)=O	1346.8	Standard non polar	33892256
L-N-Carboxymethylserine	OCC(NCC(O)=O)C(O)=O	1666.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-N-Carboxymethylserine,1TMS,isomer #1	C[Si](C)(C)OCC(NCC(=O)O)C(=O)O	1631.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TMS,isomer #2	C[Si](C)(C)OC(=O)CNC(CO)C(=O)O	1622.0	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TMS,isomer #3	C[Si](C)(C)OC(=O)C(CO)NCC(=O)O	1609.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TMS,isomer #4	C[Si](C)(C)N(CC(=O)O)C(CO)C(=O)O	1668.9	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #1	C[Si](C)(C)OCC(NCC(=O)O[Si](C)(C)C)C(=O)O	1680.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #2	C[Si](C)(C)OCC(NCC(=O)O)C(=O)O[Si](C)(C)C	1647.2	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #3	C[Si](C)(C)OCC(C(=O)O)N(CC(=O)O)[Si](C)(C)C	1729.0	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #4	C[Si](C)(C)OC(=O)CNC(CO)C(=O)O[Si](C)(C)C	1658.0	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #5	C[Si](C)(C)OC(=O)CN(C(CO)C(=O)O)[Si](C)(C)C	1715.7	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TMS,isomer #6	C[Si](C)(C)OC(=O)C(CO)N(CC(=O)O)[Si](C)(C)C	1694.8	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TMS,isomer #1	C[Si](C)(C)OCC(NCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1709.8	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TMS,isomer #2	C[Si](C)(C)OCC(C(=O)O)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1766.4	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TMS,isomer #3	C[Si](C)(C)OCC(C(=O)O[Si](C)(C)C)N(CC(=O)O)[Si](C)(C)C	1736.1	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TMS,isomer #4	C[Si](C)(C)OC(=O)CN(C(CO)C(=O)O[Si](C)(C)C)[Si](C)(C)C	1730.5	Semi standard non polar	33892256
L-N-Carboxymethylserine,4TMS,isomer #1	C[Si](C)(C)OCC(C(=O)O[Si](C)(C)C)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1794.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,4TMS,isomer #1	C[Si](C)(C)OCC(C(=O)O[Si](C)(C)C)N(CC(=O)O[Si](C)(C)C)[Si](C)(C)C	1778.9	Standard non polar	33892256
L-N-Carboxymethylserine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(NCC(=O)O)C(=O)O	1874.1	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CNC(CO)C(=O)O	1885.4	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C(CO)NCC(=O)O	1888.9	Semi standard non polar	33892256
L-N-Carboxymethylserine,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CC(=O)O)C(CO)C(=O)O	1943.5	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(NCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O	2131.0	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(NCC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C	2092.4	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC(C(=O)O)N(CC(=O)O)[Si](C)(C)C(C)(C)C	2166.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CNC(CO)C(=O)O[Si](C)(C)C(C)(C)C	2120.5	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC(=O)CN(C(CO)C(=O)O)[Si](C)(C)C(C)(C)C	2192.6	Semi standard non polar	33892256
L-N-Carboxymethylserine,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC(=O)C(CO)N(CC(=O)O)[Si](C)(C)C(C)(C)C	2183.3	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(NCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2333.0	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(C(=O)O)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2414.9	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC(C(=O)O[Si](C)(C)C(C)(C)C)N(CC(=O)O)[Si](C)(C)C(C)(C)C	2406.8	Semi standard non polar	33892256
L-N-Carboxymethylserine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(=O)CN(C(CO)C(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2391.5	Semi standard non polar	33892256
L-N-Carboxymethylserine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(C(=O)O[Si](C)(C)C(C)(C)C)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2593.6	Semi standard non polar	33892256
L-N-Carboxymethylserine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(C(=O)O[Si](C)(C)C(C)(C)C)N(CC(=O)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2560.9	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - L-N-Carboxymethylserine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00rf-9500000000-a0b470296bcfe59fe791	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-N-Carboxymethylserine GC-MS (3 TMS) - 70eV, Positive	splash10-03kc-9573000000-361773e2edcff9023327	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-N-Carboxymethylserine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-N-Carboxymethylserine 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 - L-N-Carboxymethylserine 10V, Positive-QTOF	splash10-03xs-1900000000-d9c7030551608478fab6	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 20V, Positive-QTOF	splash10-0gb9-4900000000-4210809e9a3f1b2eb141	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 40V, Positive-QTOF	splash10-0uk9-9600000000-88241356149a8b4439ab	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 10V, Negative-QTOF	splash10-03di-1900000000-2c5d8e7e3cc4e8b7d585	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 20V, Negative-QTOF	splash10-0i0r-3900000000-10598819aed0829c695e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 40V, Negative-QTOF	splash10-00dl-9300000000-e59a4854e907b49a4140	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 10V, Negative-QTOF	splash10-0hfx-1900000000-8b8da3a5b49df5a4274d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 20V, Negative-QTOF	splash10-0fy9-9800000000-0b739481f12b9f09cc32	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 40V, Negative-QTOF	splash10-05fu-9100000000-6843d3cdd9c98f15933d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 10V, Positive-QTOF	splash10-0hft-0900000000-1ae344a401779c64eb23	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 20V, Positive-QTOF	splash10-0v6r-6900000000-f07331bea605e62dd7c5	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-N-Carboxymethylserine 40V, Positive-QTOF	splash10-0a4i-9000000000-20f32efd4e244e33da12	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

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

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

FDB002247

KNApSAcK ID

Not Available

Chemspider ID

385065

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

435401

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 L-N-Carboxymethylserine (HMDB0030393)

MOL for HMDB0030393 (L-N-Carboxymethylserine)

3D MOL for HMDB0030393 (L-N-Carboxymethylserine)

3D SDF for HMDB0030393 (L-N-Carboxymethylserine)

3D-SDF for HMDB0030393 (L-N-Carboxymethylserine)

PDB for HMDB0030393 (L-N-Carboxymethylserine)

3D PDB for HMDB0030393 (L-N-Carboxymethylserine)

SMILES for HMDB0030393 (L-N-Carboxymethylserine)

INCHI for HMDB0030393 (L-N-Carboxymethylserine)

Structure for HMDB0030393 (L-N-Carboxymethylserine)

3D Structure for HMDB0030393 (L-N-Carboxymethylserine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra