T3DB: Glyceric acid

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Gene Regulation Targets (1)XML

Targets (1)

Record Information

Version

2.0

Creation Date

2014-08-29 06:28:02 UTC

Update Date

2018-03-21 17:46:17 UTC

Accession Number

T3D4330

Identification

Common Name

Glyceric acid

Class

Small Molecule

Description

Glyceric acid is a colourless syrupy acid, obtained from oxidation of glycerol. It is a compound that is secreted excessively in the urine by patients suffering from D-glyceric aciduria, an inborn error of metabolism, and D-glycerate anemia. Deficiency of human glycerate kinase leads to D-glycerate acidemia/D-glyceric aciduria. Symptoms of the disease include progressive neurological impairment, hypotonia, seizures, failure to thrive, and metabolic acidosis. At sufficiently high levels, glyceric acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Glyceric acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated glyceric aciduria. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.

Compound Type

Animal Toxin
Food Toxin
Metabolite
Natural Compound
Organic Compound

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym
(R)-glycerate
a,b-Hydroxypropionate
a,b-Hydroxypropionic acid
D-Glycerate
D-Glyceric acid
Glycerate

Chemical Formula

C₃H₆O₄

Average Molecular Mass

106.077 g/mol

Monoisotopic Mass

106.027 g/mol

CAS Registry Number

473-81-4

IUPAC Name

(2R)-2,3-dihydroxypropanoic acid

Traditional Name

glycerate

SMILES

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

InChI Identifier

InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m1/s1

InChI Key

InChIKey=RBNPOMFGQQGHHO-UWTATZPHSA-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:32398 )

Biological Properties

Status

Detected and Not Quantified

Origin

Endogenous

Cellular Locations

Cytoplasm
Extracellular

Biofluid Locations

Not Available

Tissue Locations

Prostate

Pathways

Name	SMPDB Link	KEGG Link
Glycerolipid Metabolism	SMP00039	map00561
Glycine and Serine Metabolism	SMP00004	map00260
D-glyceric acidura	SMP00529	Not Available

Applications

Not Available

Biological Roles

fundamental metabolite

Chemical Roles

Not Available

Physical Properties

State

Liquid

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	1000.0 mg/mL
LogP	Not Available

Predicted 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	8.96 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-0f6t-0910000000-52b917dbc684454452ae	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0uei-0920000000-4d5f18f14464b7289e4e	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-0f72-0920000000-7727c90167e5f1e15f7c	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0f6t-0910000000-52b917dbc684454452ae	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uei-0920000000-4d5f18f14464b7289e4e	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01po-9000000000-e74d8dcadd449f32f28f	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0avr-9362000000-4ae43a853db514e46cc7	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)	splash10-0ufr-9800000000-f68cee7fd839cc0c350a	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)	splash10-0pb9-9300000000-c9741b095b361aa0bf2e	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)	splash10-0udi-8900000000-2ca9bd370ef2f7afdf64	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-0udi-0900000000-2c68fcd2a4c9cc998e14	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0a4i-9400000000-a3e0c92f667ab9fdfbe5	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-9000000000-e2f8962c5a4a4bde459a	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-052e-9000000000-08ad44e661510838b17f	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0007-9000000000-b65c29cedef64ad74dfb	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0a4i-1900000000-2d91902f3a95d7e66bba	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0udi-0900000000-2c68fcd2a4c9cc998e14	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9400000000-a3e0c92f667ab9fdfbe5	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-e2f8962c5a4a4bde459a	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-052e-9000000000-08ad44e661510838b17f	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0007-9000000000-b65c29cedef64ad74dfb	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0a4i-1900000000-2d91902f3a95d7e66bba	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9000000000-b4845ca0075939f3095f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-052f-9000000000-f8ad6e1bbc7c43ea1122	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-9400000000-9d9a074f07f367d0a0cc	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-9300000000-0e161d242fe9a38ccf1a	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4r-9600000000-6c887f0d5bb5b5b43e47	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p9-9100000000-4dcb939c91e313be7889	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-0ddbae5fe95cd5c2cc3a	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-7900000000-483a2fcbaa1f9e4282f8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9200000000-c37acde4cab84c418b98	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-c2110468981b90e60c2b	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum

Toxicity Profile

Route of Exposure

Not Available

Mechanism of Toxicity

Glyceric acid is a compound that is secreted excessively in the urine by patients suffering from D-glyceric aciduria and D-glycerate anemia. Deficiency of human glycerate kinase leads to D-glycerate acidemia/D-glyceric aciduria. Accumulation of glyceric acid in the body has been shown to be toxic.

Metabolism

Not Available

Toxicity Values

Not Available

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

This is an endogenously produced metabolite found in the human body. It is used in metabolic reactions, catabolic reactions or waste generation.

Minimum Risk Level

Not Available

Health Effects

Chronically high levels of D-glyceric acid are associated with D-glyceric acidura.

Symptoms

Not Available

Treatment

Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

DrugBank ID

Not Available

HMDB ID

HMDB00139

PubChem Compound ID

439194

ChEMBL ID

Not Available

ChemSpider ID

388334

KEGG ID

C00258

UniProt ID

Not Available

OMIM ID

ChEBI ID

32398

BioCyc ID

2-PG

CTD ID

Not Available

Stitch ID

Not Available

PDB ID

DGY

ACToR ID

Not Available

Wikipedia Link

Glyceric acid

References

Synthesis Reference

Kyriacou, Demetrios; Tougas, Terrence P. Preparation of glyceric acid by anodic oxidation of glycerol at a silver oxide electrode. Journal of Organic Chemistry (1987), 52(11), 2318-19.

MSDS

Link

General References

Topcu M, Saatci I, Haliloglu G, Kesimer M, Coskun T: D-glyceric aciduria in a six-month-old boy presenting with West syndrome and autistic behaviour. Neuropediatrics. 2002 Feb;33(1):47-50. [11930278 ]
Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [14708889 ]
Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [8087979 ]
Dietzen DJ, Wilhite TR, Kenagy DN, Milliner DS, Smith CH, Landt M: Extraction of glyceric and glycolic acids from urine with tetrahydrofuran: utility in detection of primary hyperoxaluria. Clin Chem. 1997 Aug;43(8 Pt 1):1315-20. [9267307 ]
Fontaine M, Porchet N, Largilliere C, Marrakchi S, Lhermitte M, Aubert JP, Degand P: Biochemical contribution to diagnosis and study of a new case of D-glyceric acidemia/aciduria. Clin Chem. 1989 Oct;35(10):2148-51. [2551543 ]
Hoffmann GF, Meier-Augenstein W, Stockler S, Surtees R, Rating D, Nyhan WL: Physiology and pathophysiology of organic acids in cerebrospinal fluid. J Inherit Metab Dis. 1993;16(4):648-69. [8412012 ]
Bennett MJ, Ragni MC, Hood I, Hale DE: Comparison of post-mortem urinary and vitreous humour organic acids. Ann Clin Biochem. 1992 Sep;29 ( Pt 5):541-5. [1444166 ]
Rashed MS, Aboul-Enein HY, AlAmoudi M, Jakob M, Al-Ahaideb LY, Abbad A, Shabib S, Al-Jishi E: Chiral liquid chromatography tandem mass spectrometry in the determination of the configuration of glyceric acid in urine of patients with D-glyceric and L-glyceric acidurias. Biomed Chromatogr. 2002 May;16(3):191-8. [11920944 ]
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [19212411 ]

Gene Regulation

Up-Regulated Genes

Not Available

Down-Regulated Genes

Not Available

Targets

Target Details

1. Phosphoglycerate kinase 1

General Function:: Phosphoglycerate kinase activity
Specific Function:: In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
Gene Name:: PGK1
Uniprot ID:: P00558
Molecular Weight:: 44614.36 Da

Glyceric acid (T3D4330)

Structure for T3D4330: Glyceric acid

Targets