Bovine Metabolome Database: Showing metabocard for Glyceric acid (BMDB0000139)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:20:04 UTC

Update Date

2020-05-21 16:28:42 UTC

BMDB ID

BMDB0000139

Secondary Accession Numbers

BMDB00139

Metabolite Identification

Common Name

Glyceric acid

Description

Glyceric acid, also known as glycerate or D-groa, 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. Glyceric acid is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Glyceric acid exists in all living species, ranging from bacteria to humans. Glyceric acid is a potentially toxic compound. Glyceric acid has been found to be associated with several diseases known as irritable bowel syndrome, ulcerative colitis, and eosinophilic esophagitis; also glyceric acid has been linked to several inborn metabolic disorders including primary hyperoxaluria and primary hyperoxaluria II.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
alpha,beta-Hydroxypropionic acid	ChEBI
D-GroA	ChEBI
R-Glyceric acid	ChEBI
Glycerate	Kegg
(R)-Glycerate	Kegg
a,b-Hydroxypropionate	Generator
a,b-Hydroxypropionic acid	Generator
alpha,beta-Hydroxypropionate	Generator
R-Glycerate	Generator
(R)-Glyceric acid	Generator
D-Glycerate	HMDB
D-Glyceric acid	HMDB
(2R)-2,3-Dihydroxypropanoic acid	HMDB
(R)-2,3-Dihydroxypropanoic acid	HMDB
D-2,3-Dihydroxypropanoic acid	HMDB

Chemical Formula

C₃H₆O₄

Average Molecular Weight

106.0773

Monoisotopic Molecular Weight

106.02660868

IUPAC Name

(2R)-2,3-dihydroxypropanoic acid

Traditional Name

glycerate

CAS Registry Number

473-81-4

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-/m1/s1

InChI Key

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 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cytoplasm
Mitochondria

Physical Properties

State

Liquid

Experimental Properties

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

Predicted Properties

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

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria

Biospecimen Locations

Liver
Mammary Gland
Milk
Placenta
Prostate Tissue
Urine

Pathways

Name	SMPDB/Pathwhiz	KEGG
Glycerolipid Metabolism		Not Available
Glycine and Serine Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Characterization ...	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Kurt J. Boudonck,...	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 25599412	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000139

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

32398

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.

Material Safety Data Sheet (MSDS)

Not Available

General References

Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff and John A. Ryals (2009). Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff, John A. Ryals. Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics (2009) 5:375-386 doi: 10.1007/s11306-009-0160-8. Metabolomics.
Kurt J. Boudonck, Matthew W. Mitchell, Jacob Wulff, John A. Ryals (2009). Characterization of the biochemical variability of bovine milk using metabolomics. Metabolomics.

Enzymes

Enzyme Details

1. Aldehyde dehydrogenase family 3 member B1

General function:: Energy production and conversion
Specific function:: Oxidizes medium and long chain saturated and unsaturated aldehydes. Metabolizes also benzaldehyde. Low activity towards acetaldehyde and 3,4-dihydroxyphenylacetaldehyde. May not metabolize short chain aldehydes. Can use both NADP(+) and NAD(+) as electron acceptor. May have a protective role against the cytotoxicity induced by lipid peroxidation.
Gene Name:: ALDH3B1
Uniprot ID:: Q1JPA0
Molecular weight:: 51800.0

Reactions

Glyceric acid + NADP + Water → Glyceraldehyde + NADPH	details

Enzyme Details

2. Glycerate kinase

General function:: Carbohydrate transport and metabolism
Specific function:: Not Available
Gene Name:: GLYCTK
Uniprot ID:: Q2KJF7
Molecular weight:: 54720.0

Reactions

3-Phosphoglyceric acid + Adenosine triphosphate → Glyceric acid + ADP	details
Glyceric acid + Adenosine triphosphate → 3-Phosphoglyceric acid + ADP	details

Showing metabocard for Glyceric acid (BMDB0000139)

Structure for BMDB0000139 (Glyceric acid)

Enzymes

Reactions

Reactions