Showing Compound Card for Glyceric acid (CDB006164)

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Record Information
Version1.0
Created at2020-03-18 23:22:13 UTC
Updated at2022-12-13 23:36:27 UTC
CannabisDB IDCDB006164
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameGlyceric acid
DescriptionGlyceric acid is a colourless syrupy acid, obtained via the oxidation of glycerol. Glyceric acid is a weak 3-carbon sugar acid. Several phosphate derivatives of glyceric acid, including 2-phosphoglyceric acid, 3-phosphoglyceric acid, 2,3-bisphosphoglyceric acid, and 1,3-bisphosphoglyceric acid, are important biochemical intermediates in glycolysis. In particular, 3-phosphoglyceric acid is an important molecule for the biosynthesis of the amino acid serine, which in turn can be used in the synthesis of glycine and cysteine. Glyceric acid is not normally found in human biofluids, however high levels are secreted in the urine by patients suffering from D-glyceric aciduria, an inborn error of metabolism. It is also elevated in the serum of individuals suffering from D-glycerate anemia. A deficiency of human glycerate kinase has been shown to lead to D-glycerate acidemia/D-glyceric aciduria ( PMID: 20949620 ). 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. Abnormally high levels of organic acids (glyceric acid is an organic acid) 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. Elevated values may also be due to microbial sources such as yeast (Aspergillus, Penicillium, probably Candida) or due to dietary sources containing glycerol (glycerine). Glyceric acid can be isolated from various crop plants (e.g. brassicas and pulses) and has also been found in peanuts, artichokes, tomatoes, apples, bananas, broad beans and grapes (PMID: 19621222 ).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
alpha,beta-Hydroxypropionic acidChEBI
D-GroAChEBI
R-Glyceric acidChEBI
GlycerateKegg
(R)-GlycerateKegg
a,b-HydroxypropionateGenerator
a,b-Hydroxypropionic acidGenerator
alpha,beta-HydroxypropionateGenerator
R-GlycerateGenerator
(R)-Glyceric acidGenerator
D-GlycerateHMDB
D-Glyceric acidHMDB
(2R)-2,3-Dihydroxypropanoic acidHMDB
(R)-2,3-Dihydroxypropanoic acidHMDB
D-2,3-Dihydroxypropanoic acidHMDB
Chemical FormulaC3H6O4
Average Molecular Weight106.08
Monoisotopic Molecular Weight106.0266
IUPAC Name(2R)-2,3-dihydroxypropanoic acid
Traditional Nameglycerate
CAS Registry Number6000-40-4
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 KeyRBNPOMFGQQGHHO-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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar 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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Indirect biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point<25 °CWikipedia
Boiling Point412 °CWikipedia
Water Solubility1000 mg/mLNot Available
logP-1.723Wikipedia
Predicted Properties
PropertyValueSource
logP-1.7ALOGPS
logP-1.5ChemAxon
logS0.78ALOGPS
pKa (Strongest Acidic)3.42ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.38 m³·mol⁻¹ChemAxon
Polarizability8.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MSGlyceric acid, non-derivatized, GC-MS Spectrumsplash10-0f6t-0910000000-52b917dbc684454452aeSpectrum
GC-MSGlyceric acid, 3 TMS, GC-MS Spectrumsplash10-0uei-0920000000-4d5f18f14464b7289e4eSpectrum
GC-MSGlyceric acid, non-derivatized, GC-MS Spectrumsplash10-0f72-0920000000-7727c90167e5f1e15f7cSpectrum
GC-MSGlyceric acid, non-derivatized, GC-MS Spectrumsplash10-0f6t-0910000000-52b917dbc684454452aeSpectrum
GC-MSGlyceric acid, non-derivatized, GC-MS Spectrumsplash10-0uei-0920000000-4d5f18f14464b7289e4eSpectrum
Predicted GC-MSGlyceric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-01po-9000000000-e74d8dcadd449f32f28fSpectrum
Predicted GC-MSGlyceric acid, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0avr-9362000000-4ae43a853db514e46cc7Spectrum
Predicted GC-MSGlyceric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSGlyceric acid, TBDMS_3_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-0ufr-9800000000-f68cee7fd839cc0c350a2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0pb9-9300000000-c9741b095b361aa0bf2e2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-0udi-8900000000-2ca9bd370ef2f7afdf642012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0udi-0900000000-2c68fcd2a4c9cc998e142012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0a4i-9400000000-a3e0c92f667ab9fdfbe52012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0a4i-9000000000-e2f8962c5a4a4bde459a2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-052e-9000000000-08ad44e661510838b17f2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0007-9000000000-b65c29cedef64ad74dfb2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0a4i-1900000000-2d91902f3a95d7e66bba2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0udi-0900000000-2c68fcd2a4c9cc998e142017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9400000000-a3e0c92f667ab9fdfbe52017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a4i-9000000000-e2f8962c5a4a4bde459a2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-052e-9000000000-08ad44e661510838b17f2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0007-9000000000-b65c29cedef64ad74dfb2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0a4i-1900000000-2d91902f3a95d7e66bba2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-9000000000-b4845ca0075939f3095f2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-052f-9000000000-f8ad6e1bbc7c43ea11222021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-9400000000-9d9a074f07f367d0a0cc2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-9300000000-0e161d242fe9a38ccf1a2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4r-9600000000-6c887f0d5bb5b5b43e472016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01p9-9100000000-4dcb939c91e313be78892016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-0ddbae5fe95cd5c2cc3a2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-7900000000-483a2fcbaa1f9e4282f82016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-9200000000-c37acde4cab84c418b982016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-c2110468981b90e60c2b2016-09-12View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
Glycerate kinaseGLYCTK3p21.1Q8IVS8 details
TransportersNot Available
Metal BindingsNot Available
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Cannabis CultivarStatusValueReferenceDetails
Alien DawgDetected and Quantified0.158 mg/g dry wt
    • David S. Wishart,...
 details
GabriolaDetected and Quantified0.0624 mg/g dry wt
    • David S. Wishart,...
 details
Island HoneyDetected and Quantified0.199 mg/g dry wt
    • David S. Wishart,...
 details
QuadraDetected and Quantified0.246 mg/g dry wt
    • David S. Wishart,...
 details
Sensi StarDetected and Quantified0.314 mg/g dry wt
    • David S. Wishart,...
 details
Tangerine DreamDetected and Quantified0.243 mg/g dry wt
    • David S. Wishart,...
 details
HMDB IDHMDB0000139
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012242
KNApSAcK IDC00001185
Chemspider ID388334
KEGG Compound IDC00258
BioCyc IDGLYCERATE
BiGG ID34424
Wikipedia LinkGlyceric acid
METLIN ID280
PubChem Compound439194
PDB IDNot Available
ChEBI ID32398
References
General References
  1. Habe H, Fukuoka T, Kitamoto D, Sakaki K: Biotechnological production of D-glyceric acid and its application. Appl Microbiol Biotechnol. 2009 Sep;84(3):445-52. doi: 10.1007/s00253-009-2124-3. Epub 2009 Jul 21. [PubMed:19621222 ]
  2. Sass JO, Fischer K, Wang R, Christensen E, Scholl-Burgi S, Chang R, Kapelari K, Walter M: D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK). Hum Mutat. 2010 Dec;31(12):1280-5. doi: 10.1002/humu.21375. Epub 2010 Nov 9. [PubMed:20949620 ]

Enzymes

Enzyme Details
1. Glycerate kinase
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
GLYCTK
Uniprot ID:
Q8IVS8
Molecular weight:
25036.865