Cannabis Compound Database: Showing Compound Card for Glyceric acid (CDB006164)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (1) Show 1 protein XML

Record Information

Version

1.0

Created at

2020-03-18 23:22:13 UTC

Updated at

2020-12-07 19:06:57 UTC

CannabisDB ID

CDB006164

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

Glyceric acid

Description

Glyceric 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

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

106.08

Monoisotopic Molecular Weight

106.0266

IUPAC Name

(2R)-2,3-dihydroxypropanoic acid

Traditional Name

glycerate

CAS Registry Number

6000-40-4

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 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

Ingestion

Fabaceae

Biological location:

Tissue and substructures:

Placenta

Cell and elements:

Extracellular

Organ and components:

Prostate

Biofluid and excreta:

Subcellular:

Role

Indirect biological role:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	<25 °C	Wikipedia
Boiling Point	412 °C	Wikipedia
Water Solubility	1000 mg/mL	Not Available
logP	-1.723	Wikipedia

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	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	Glyceric acid, non-derivatized, GC-MS Spectrum	splash10-0f6t-0910000000-52b917dbc684454452ae	Spectrum
GC-MS	Glyceric acid, 3 TMS, GC-MS Spectrum	splash10-0uei-0920000000-4d5f18f14464b7289e4e	Spectrum
GC-MS	Glyceric acid, non-derivatized, GC-MS Spectrum	splash10-0f72-0920000000-7727c90167e5f1e15f7c	Spectrum
GC-MS	Glyceric acid, non-derivatized, GC-MS Spectrum	splash10-0f6t-0910000000-52b917dbc684454452ae	Spectrum
GC-MS	Glyceric acid, non-derivatized, GC-MS Spectrum	splash10-0uei-0920000000-4d5f18f14464b7289e4e	Spectrum
Predicted GC-MS	Glyceric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-01po-9000000000-e74d8dcadd449f32f28f	Spectrum
Predicted GC-MS	Glyceric acid, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0avr-9362000000-4ae43a853db514e46cc7	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)	splash10-0ufr-9800000000-f68cee7fd839cc0c350a	Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)	splash10-0pb9-9300000000-c9741b095b361aa0bf2e	Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)	splash10-0udi-8900000000-2ca9bd370ef2f7afdf64	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative	splash10-0udi-0900000000-2c68fcd2a4c9cc998e14	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative	splash10-0a4i-9400000000-a3e0c92f667ab9fdfbe5	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative	splash10-0a4i-9000000000-e2f8962c5a4a4bde459a	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negative	splash10-052e-9000000000-08ad44e661510838b17f	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negative	splash10-0007-9000000000-b65c29cedef64ad74dfb	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-0a4i-1900000000-2d91902f3a95d7e66bba	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0udi-0900000000-2c68fcd2a4c9cc998e14	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9400000000-a3e0c92f667ab9fdfbe5	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0a4i-9000000000-e2f8962c5a4a4bde459a	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-052e-9000000000-08ad44e661510838b17f	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0007-9000000000-b65c29cedef64ad74dfb	Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-0a4i-1900000000-2d91902f3a95d7e66bba	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4r-9600000000-6c887f0d5bb5b5b43e47	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p9-9100000000-4dcb939c91e313be7889	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-0ddbae5fe95cd5c2cc3a	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-7900000000-483a2fcbaa1f9e4282f8	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9200000000-c37acde4cab84c418b98	Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-c2110468981b90e60c2b	Spectrum

NMR

Type	Description		View
1D NMR	1H NMR Spectrum		Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum		Spectrum

Pathways

Name	SMPDB/Pathwhiz	KEGG
Glycine and Serine Metabolism
Glycerolipid Metabolism
Glycerol Kinase Deficiency		Not Available
D-glyceric acidura		Not Available
Familial lipoprotein lipase deficiency		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Glycerate kinase	GLYCTK	3p21.1	Q8IVS8	details

Transporters

Not Available

Metal Bindings

Not Available

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Cannabis Cultivar	Status	Value	Reference	Details
Alien Dawg	Detected and Quantified	1.49 mg/g dry wt	Jiamin Zheng, Yil...	details
Gabriola	Detected and Quantified	0.588 mg/g dry wt	Jiamin Zheng, Yil...	details
Island Honey	Detected and Quantified	1.88 mg/g dry wt	Jiamin Zheng, Yil...	details
Quadra	Detected and Quantified	2.32 mg/g dry wt	Jiamin Zheng, Yil...	details
Sensi Star	Detected and Quantified	2.96 mg/g dry wt	Jiamin Zheng, Yil...	details
Tangerine Dream	Detected and Quantified	2.29 mg/g dry wt	Jiamin Zheng, Yil...	details

External Links

HMDB ID

HMDB0000139

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

General References

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 ]
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

Showing Compound Card for Glyceric acid (CDB006164)

Structure for CDB006164 (Glyceric acid)

Enzymes