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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2007-05-23 02:57:34 UTC

Update Date

2021-09-14 15:44:52 UTC

HMDB ID

HMDB0006372

Secondary Accession Numbers

HMDB06372

Metabolite Identification

Common Name

L-Glyceric acid

Description

L-glyceric acid is a human urinary metabolite present in patients with L-Glyceric aciduria. The formation of L-glyceric acid from accumulated hydroxypyruvate is due to deficiency of human glyoxylate reductase/hydroxypyruvate reductase (GRHPR, EC 1.1.1.81), a D-2-hydroxy-acid dehydrogenase that plays a critical role in the removal of the metabolic by-product glyoxylate from within the liver. Deficiency of this enzyme is the underlying cause of primary hyperoxaluria type 2 (PH2) and leads to increased urinary oxalate levels, formation of kidney stones and renal failure. (PMID: 16756993 ).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(S)-Glyceric acid	ChEBI
(S)-Glycerate	Generator
L-Glycerate	Generator
(2S)-2,3-Dihydroxy-propanoate	HMDB
(2S)-2,3-Dihydroxy-propanoic acid	HMDB
(S)-2,3-Dihydroxy-propanoate	HMDB
(S)-2,3-Dihydroxy-propanoic acid	HMDB
(S)-2,3-Dihydroxypropanoate	HMDB
(S)-2,3-Dihydroxypropanoic acid	HMDB

Chemical Formula

C₃H₆O₄

Average Molecular Weight

106.0773

Monoisotopic Molecular Weight

106.02660868

IUPAC Name

(2S)-2,3-dihydroxypropanoic acid

Traditional Name

L-glycerate

CAS Registry Number

28305-26-2

SMILES

OC[C@H](O)C(O)=O

InChI Identifier

InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m0/s1

InChI Key

RBNPOMFGQQGHHO-REOHCLBHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Glyceric_acid
Sugar acid
Alpha-hydroxy acid
Hydroxy acid
Monosaccharide
1,2-diol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Organic oxide
Primary alcohol
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

glyceric acid (CHEBI:74324 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	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	639 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.5	ChemAxon
logS	0.78	ALOGPS
pKa (Strongest Acidic)	3.42	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	20.38 m³·mol⁻¹	ChemAxon
Polarizability	8.94 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]+	120.604	31661259
DarkChem	[M-H]-	115.647	31661259
DeepCCS	[M+H]+	118.46	30932474
DeepCCS	[M-H]-	115.66	30932474
DeepCCS	[M-2H]-	152.106	30932474
DeepCCS	[M+Na]+	126.791	30932474
AllCCS	[M+H]+	128.0	32859911
AllCCS	[M+H-H2O]+	123.7	32859911
AllCCS	[M+NH4]+	132.0	32859911
AllCCS	[M+Na]+	133.1	32859911
AllCCS	[M-H]-	120.7	32859911
AllCCS	[M+Na-2H]-	124.5	32859911
AllCCS	[M+HCOO]-	128.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
L-Glyceric acid	OC[C@H](O)C(O)=O	2227.6	Standard polar	33892256
L-Glyceric acid	OC[C@H](O)C(O)=O	1044.9	Standard non polar	33892256
L-Glyceric acid	OC[C@H](O)C(O)=O	1100.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
L-Glyceric acid,1TMS,isomer #1	C[Si](C)(C)OC[C@H](O)C(=O)O	1155.8	Semi standard non polar	33892256
L-Glyceric acid,1TMS,isomer #2	C[Si](C)(C)O[C@@H](CO)C(=O)O	1189.2	Semi standard non polar	33892256
L-Glyceric acid,1TMS,isomer #3	C[Si](C)(C)OC(=O)[C@@H](O)CO	1085.5	Semi standard non polar	33892256
L-Glyceric acid,2TMS,isomer #1	C[Si](C)(C)OC[C@H](O[Si](C)(C)C)C(=O)O	1258.6	Semi standard non polar	33892256
L-Glyceric acid,2TMS,isomer #2	C[Si](C)(C)OC[C@H](O)C(=O)O[Si](C)(C)C	1223.2	Semi standard non polar	33892256
L-Glyceric acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)[C@H](CO)O[Si](C)(C)C	1220.3	Semi standard non polar	33892256
L-Glyceric acid,3TMS,isomer #1	C[Si](C)(C)OC[C@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1328.0	Semi standard non polar	33892256
L-Glyceric acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](O)C(=O)O	1419.6	Semi standard non polar	33892256
L-Glyceric acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H](CO)C(=O)O	1442.1	Semi standard non polar	33892256
L-Glyceric acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](O)CO	1338.7	Semi standard non polar	33892256
L-Glyceric acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1703.4	Semi standard non polar	33892256
L-Glyceric acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H](O)C(=O)O[Si](C)(C)C(C)(C)C	1658.5	Semi standard non polar	33892256
L-Glyceric acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@H](CO)O[Si](C)(C)C(C)(C)C	1675.1	Semi standard non polar	33892256
L-Glyceric acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1960.9	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 - L-Glyceric acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-01po-9000000000-88f14f02029fc1ed3f09	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Glyceric acid GC-MS (3 TMS) - 70eV, Positive	splash10-0avr-9362000000-4ae43a853db514e46cc7	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - L-Glyceric acid 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-Glyceric acid 10V, Positive-QTOF	splash10-0a4r-9600000000-6c887f0d5bb5b5b43e47	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 20V, Positive-QTOF	splash10-01p9-9100000000-4dcb939c91e313be7889	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 40V, Positive-QTOF	splash10-0006-9000000000-0ddbae5fe95cd5c2cc3a	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 10V, Negative-QTOF	splash10-0a4i-7900000000-483a2fcbaa1f9e4282f8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 20V, Negative-QTOF	splash10-0a4i-9200000000-c37acde4cab84c418b98	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 40V, Negative-QTOF	splash10-0a4l-9000000000-c2110468981b90e60c2b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 10V, Positive-QTOF	splash10-00du-9000000000-e4b00c30702ce3ea058c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 20V, Positive-QTOF	splash10-006x-9000000000-88e9a7bbb2eae9f5a36b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 40V, Positive-QTOF	splash10-0006-9000000000-cbe41726597364826475	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 10V, Negative-QTOF	splash10-0a6r-9700000000-e74837163c200bdac143	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 20V, Negative-QTOF	splash10-0a6r-9000000000-3d8e20cb2f7b52d78388	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - L-Glyceric acid 40V, Negative-QTOF	splash10-052f-9000000000-54fe1ddd9f87bf26bf84	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

Cytoplasm
Extracellular

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	2.0 (0.0-5.0) uM	Adult (>18 years old)	Both	Normal	1458609	details
Urine	Detected and Quantified	23.448-89.529 umol/mmol creatinine	Children (1-13 years old)	Male	Normal	8311084	details
Urine	Detected and Quantified	39.436-197.178 umol/mmol creatinine	Adult (>18 years old)	Female	Normal	8311084	details
Urine	Detected and Quantified	12.8-187.1 umol/mmol creatinine	Children (1-13 years old)	Both	Normal	9267307	details
Urine	Detected and Quantified	20.3-121.6 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	9267307	details
Urine	Detected and Quantified	0-205 umol/mmol creatinine	Children (1-13 years old)	Both	Normal	Primary Hyperoxal...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	3.0 (0.0-5.0) uM	Adult (>18 years old)	Both	Glycolic aciduria	1458609	details
Urine	Detected and Quantified	430.594 umol/mmol creatinine	Children (1-13 years old)	Male	Glutaric acidemia type 2	8311084	details
Urine	Detected and Quantified	590.468-4130.0778 umol/mmol creatinine	Adult (>18 years old)	Female	Glutaric acidemia type 2	8311084	details
Urine	Detected and Quantified	>205 umol/mmol creatinine	Children (1-13 years old)	Both	Glycolic aciduria	Primary Hyperoxal...	details

Associated Disorders and Diseases

Disease References

Glycolic aciduria
Petrarulo M, Marangella M, Cosseddu D, Linari F: High-performance liquid chromatographic assay for L-glyceric acid in body fluids. Application in primary hyperoxaluria type 2. Clin Chim Acta. 1992 Oct 30;211(3):143-53. [PubMed:1458609 ] Coulter-Mackie MB, White CT, Lange D, et al. (2002). Primary Hyperoxaluria Type 1. 2002 Jun 19 [Updated 2014 Jul 17]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1283/. University of Washington, Seattle.
Glutaric acidemia type 2
Chlebeck PT, Milliner DS, Smith LH: Long-term prognosis in primary hyperoxaluria type II (L-glyceric aciduria). Am J Kidney Dis. 1994 Feb;23(2):255-9. [PubMed:8311084 ]

Associated OMIM IDs

259900 (Glycolic aciduria)
231680 (Glutaric acidemia type 2)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023907

KNApSAcK ID

Not Available

Chemspider ID

4885497

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

2226325

Wikipedia Link

Glyceric acid

METLIN ID

Not Available

PubChem Compound

6326776

PDB ID

Not Available

ChEBI ID

74324

Food Biomarker Ontology

Not Available

VMH ID

GLYC_S

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Lok, C. M.; Ward, J. P.; Van Dorp, D. A. The synthesis of chiral glycerides starting from D- and L-serine. Actes Congr. Mond. - Soc. Int. Etude Corps Gras, 13th (1976), Sect. E 15-20.

Material Safety Data Sheet (MSDS)

Not Available

General References

Booth MP, Conners R, Rumsby G, Brady RL: Structural basis of substrate specificity in human glyoxylate reductase/hydroxypyruvate reductase. J Mol Biol. 2006 Jun 30;360(1):178-89. Epub 2006 May 22. [PubMed:16756993 ]

Showing metabocard for L-Glyceric acid (HMDB0006372)

MOL for HMDB0006372 (L-Glyceric acid)

3D MOL for HMDB0006372 (L-Glyceric acid)

3D SDF for HMDB0006372 (L-Glyceric acid)

3D-SDF for HMDB0006372 (L-Glyceric acid)

PDB for HMDB0006372 (L-Glyceric acid)

3D PDB for HMDB0006372 (L-Glyceric acid)

SMILES for HMDB0006372 (L-Glyceric acid)

INCHI for HMDB0006372 (L-Glyceric acid)

Structure for HMDB0006372 (L-Glyceric acid)

3D Structure for HMDB0006372 (L-Glyceric acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra