MiMeDB: Showing metabocard for Glyceric acid (MMDBc0000041)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:28:13 UTC

Update Date

2022-08-30 23:13:59 UTC

Metabolite ID

MMDBc0000041

Metabolite Identification

Common Name

Glyceric acid

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. 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 is isolated from various plants (e.g. brassicas, pulses, and Vicia faba).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D 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

Molecular Formula

C₃H₆O₄

Average Mass

106.0773

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-04	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Placenta
Prostate
Saliva
Sweat
Urine

Tissue Locations

Placenta
Prostate

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191961	4-trimethylaminobutyraldehyde dehydrogenase	Unknown	P49189	Homo sapiens
MMDBp0191963	Alpha-aminoadipic semialdehyde dehydrogenase	Unknown	P49419	Homo sapiens
MMDBp0191964	Aldehyde dehydrogenase family 1 member A3	Unknown	P47895	Homo sapiens
MMDBp0191965	Aldehyde dehydrogenase, mitochondrial	Unknown	P05091	Homo sapiens
MMDBp0191966	Fatty aldehyde dehydrogenase	Unknown	P51648	Homo sapiens
MMDBp0191967	Aldehyde dehydrogenase X, mitochondrial	Unknown	P30837	Homo sapiens
MMDBp0192058	Glyoxylate reductase/hydroxypyruvate reductase	Unknown	Q9UBQ7	Homo sapiens
MMDBp0194168	Glycerate kinase	Enzyme	Q8IVS8	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0001355	Adenosine triphosphate	2-Phospho-D-glyceric acid	Not Available	Glycerate Kinase	VMH	30371894
MMDBr0001464	Hydrogen Ion	Glyceric acid	Glyoxylate reductase/hydroxypyruvate reductase	Hydroxypyruvate Reductase (NADPH)	VMH	30371894
MMDBr0002514	Adenosine triphosphate	3-Phospho-D-glycerate	Glycerate kinase	ATP:(R)-Glycerate 3-Phosphotransferase	VMH	30371894
MMDBr0002535	D-Glyceraldehyde	Glyceric acid	Aldehyde dehydrogenase 1 family, member b1	D-Glyceraldehyde:NAD+ Oxidoreductase	VMH	30371894
MMDBr0006029	Glyceric acid	Glyceric acid	Not Available	Transport of D-Glycerate, Diffusion	VMH	30371894
MMDBr0007672	2-Hydroxy-3-oxopropanoate	Glyceric acid	Not Available	Tartronate semialdehyde reductase	VMH	30371894
MMDBr0007673	Adenosine triphosphate	3-Phospho-D-glycerate	Not Available	ATP:(R)-Glycerate 3-Phosphotransferase Ec:2.7.1.31	VMH	30371894
MMDBr0007984	2-Hydroxy-3-oxopropanoate	Glyceric acid	Not Available	Tartronate semialdehyde reductase, NADP	VMH	30371894
MMDBr0008014	D-Glyceraldehyde	Glyceric acid	Not Available	D-Glyceraldehyde:NAD+ Oxidoreductase Ec:1.2.1.3	VMH	30371894
MMDBr0008100	Hydrogen Ion	Glyceric acid	Not Available	Glycerate dehydrogenase	VMH	30371894
MMDBr0008101	Hydrogen Ion	Glyceric acid	Not Available	Glycerate dehydrogenase (NADP)	VMH	30371894
MMDBr0010944	D-Glyceraldehyde	Glyceric acid	Not Available	Aldehyde dehydrogenase D glyceraldehyde NAD	VMH	30371894
MMDBr0013208	Tartaric acid	Glyceric acid	Probable tartrate dehydrogenase/decarboxylase	Decarboxylation	RHEA	34755880
MMDBr0013699	Glyceric acid	3-hydroxypyruvic acid	Glycerate dehydrogenase	Dehydrogenation; Reduction	RHEA	34755880
MMDBr0013700	3-hydroxypyruvic acid	Glyceric acid	Glyoxylate reductase 1	Reduction	RHEA	34755880
MMDBr0013798	Glyceric acid	3-hydroxypyruvic acid	Glyoxylate/hydroxypyruvate reductase A	Reduction	RHEA	34755880
MMDBr0013799	3-hydroxypyruvic acid	Glyceric acid	Glyoxylate reductase 1	Reduction	RHEA	34755880
MMDBr0013813	Glyceric acid	2-Hydroxy-3-oxopropanoate	2-hydroxy-3-oxopropionate reductase	Reduction	RHEA	34755880
MMDBr0013814	Glyceric acid	2-Hydroxy-3-oxopropanoate	2-hydroxy-3-oxopropionate reductase	Reduction	RHEA	34755880
MMDBr0014346	Glyceric acid	(2R)-3-phosphoglyceric acid	Glycerate kinase	Phosphorylation	RHEA	34755880
MMDBr0014672	Glyceric acid	(2R)-2-phosphoglyceric acid	Glycerate 2-kinase	Phosphorylation	RHEA	34755880
MMDBr0014673	Glyceric acid	(2R)-2-phosphoglyceric acid	Glycerate 2-kinase	Phosphorylation	RHEA	34755880
MMDBr0014744	(2R)-2-O-(6-phospho-alpha-D-mannosyl)-glyceric acid	Glyceric acid	Putative mannosylglycerate hydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0015002	Glyceric acid	(2R)-2-O-(alpha-D-mannosyl)-glyceric acid	Mannosylglycerate synthase	Synthesis	RHEA	34755880
MMDBr0015021	Glyceric acid	(2R)-2-O-(alpha-D-glucopyranosyl)-glyceric acid	Glucosylglycerate synthase	Synthesis	RHEA	34755880
MMDBr0015110	(2R)-2-O-(alpha-D-glucopyranosyl)-glyceric acid	Glyceric acid	Glucosylglycerate hydrolase	Hydrolysis of bond	RHEA	34755880
MMDBr0015732	D-Glyceraldehyde	Glyceric acid	D-glyceraldehyde dehydrogenase (NADP(+))	Dehydrogenation	RHEA	34755880
MMDBr0016795	(2R)-2-O-(alpha-D-glucopyranosyl)-glyceric acid	Glyceric acid	Glucosylglycerate phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0018164	Hydrogen Ion	Glyceric acid	2-hydroxy-3-oxopropionate reductase	Reduction	PathBank	31602464
MMDBr0018165	Glyceric acid	Hydrogen Ion	Glycerate 2-kinase	Phosphorylation	PathBank	31602464
MMDBr0018348	Hydrogen Ion	Glyceric acid	2-hydroxy-3-oxopropionate reductase	Reduction	PathBank	31602464
MMDBr0018349	Glyceric acid	Hydrogen Ion	Glycerate 2-kinase	Phosphorylation	PathBank	31602464
MMDBr0019358	Water	Glyceric acid	Mannosylglycerate hydrolase	Hydrolysis of bond	PathBank	31602464
MMDBr0019359	Glyceric acid	Hydrogen Ion	Glycerate 2-kinase	Phosphorylation	PathBank	31602464
MMDBr0019545	Glyceric acid	Water	Aldehyde dehydrogenase [NAD(P)+] 2	Dehydrogenation	PathBank	31602464
MMDBr0019546	3-Phosphoglyceric acid	Glyceric acid	D-glycerate 3-kinase	Phosphorylation	PathBank	31602464
MMDBr0024947	Water	Hydrogen Ion	Glyceraldehyde dehydrogenase large chain	Dehydrogenation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
D-glyceric acidemia	Increased	Association	Human Urine	HMDB	2165585
Primary hyperoxaluria ii	Slight Increase	Association	Human Urine	HMDB	9267307
Eosinophilic esophagitis		Association	Human Urine	HMDB	Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	387	Human stool; Human ; Human feces; Human urine; Human sputum; Human saliva; Human subgingival plaque; Human vaginal fluid; Human supragingival plaque; Human mucosa; Human pleural fluid plaque; Pig ; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Verrucomicrobia	2	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	235	Human feces; Human stool; Human ; Human feces; pleural fluid plaque; bal; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Archaea	Euryarchaeota	4	Human feces; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Bacteroidetes	105	Human feces; Human stool; Human appendix biopsy; Human ; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Actinobacteria	117	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	2	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	16	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/NULL	Proteobacteria	2	Human feces; Human stool; Human ; Human feces; pleural fluid plaque; bal; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Thermotogae	2
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Unknown
Archaea/Archaea	Euryarchaeota	3	Human feces; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Deinococcus-thermus	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Urine	Detected and Quantified			2900	5220	umol/mmol creatinine	Children (1-13 years old)	Both	D-Glyceric acidura	HMDB	2165585
Human Blood	Detected and Quantified			186	315	uM	Children (1-13 years old)	Both	D-Glyceric acidura	HMDB	2165585
Human Urine	Detected and Quantified	2360.0		1.2	1450.0	umol/mmol creatinine	Adult (>18 years old)	Both	Primary Hyperoxaluria II, PH2	HMDB	9267307
Human Urine	Detected and Quantified	4.1				umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	14708889
Human Urine	Detected and Quantified	18.9				umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	14708889
Human Urine	Detected and Quantified	20.4				umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	14708889
Human Blood	Detected and Quantified	<5				uM	Adult (>18 years old)	Both	Normal	HMDB	21359215
Human Urine	Detected and Quantified			0	0.9	umol/mmol creatinine	Infant (0-1 year old)	Male	Normal	HMDB	31963255
Human Urine	Detected and Quantified			0	2	umol/mmol creatinine	Infant (0-1 year old)	Female	Normal	HMDB	31963255
Human Urine	Detected and Quantified			1.0	1.8	umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	27012787
Human Urine	Detected and Quantified			1.5	2.1	umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	27012787
Human Urine	Detected and Quantified	1.7		0.2	6.0	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	2702744
Human Blood	Detected and Quantified	10.0		0.0	24.0	uM	Adult (>18 years old)	Both	Normal	HMDB	8412012
Human Urine	Detected and Quantified	14.4		7.8	28.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	15.9		7.8	31.1	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified	21.6		0.5	91.1	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	3.5		0.1	8.0	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	3.5		2.8	4.2	umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	HMDB	14708889
Human Cerebrospinal fluid (csf)	Detected and Quantified	34.0	34.0			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	8412012
Human Urine	Detected and Quantified	5.3		0.1	37.3	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	8.9		2.4	60.0	umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	85.303	85.515			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Eosinophilic esophagitis	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Urine	Detected and Quantified	15000.0		10000.0	20000.0	umol/mmol creatinine	Children (1-13 years old)	Both	D-Glyceric acidura	HMDB	MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de)
Human Urine	Detected and Quantified	61.247	35.4			umol/mmol creatinine	Children (1 - 13 years old)	Not Specified	Normal	HMDB	Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work)
Human Saliva	Detected and Quantified	8.20	3.95			uM	Adult (>18 years old)	Both	Normal	HMDB	Zerihun T. Dame, Farid Aziat, Rupasri Mandal, Ram Krishnamurthy, Souhaila Bouatra, Shima Borzouie, An Chi Guo, Tanvir Sajed, Lu Deng, Hong Lin, Philip Liu, Edison Dong, David S. Wishart "The human saliva metabolome" Metabolomics (2015) DOI 10.1007/s11306-015-0840-5
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Male	Normal	HMDB	22308371
Human Feces	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	20669995
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	21330412
Human Feces	Detected but not Quantified						Infant (0-1 year old)	Both	Normal	HMDB	22411374
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	22024767
Human Sweat	Detected but not Quantified						Adult	Both	Normal	HMDB	26755145
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	24801555
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	24801555
Human Blood	Detected but not Quantified						Adult (>18 years old)	Female	Normal	HMDB	27355821
Human Blood	Detected but not Quantified						Adult (>18 years old)	Female	Normal	HMDB	27355821
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	28842642
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	28157703
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

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. doi: 10.1055/s-2002-23600. [PubMed: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. doi: 10.1515/CCLM.2003.248. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. doi: 10.1007/BF00711898. [PubMed: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. doi: 10.1177/000456329202900509. [PubMed: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. doi: 10.1002/bmc.126. [PubMed: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. [PubMed:19212411 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
Yannai, Shmuel (2004). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. Boca Raton: Chapman & Hall/CRC..

Showing metabocard for Glyceric acid (MMDBc0000041)

MOL for #<Metabolite:0x00007f5a88025758>

3D MOL for #<Metabolite:0x00007f5a88025758>

3D SDF for #<Metabolite:0x00007f5a88025758>

3D-SDF for #<Metabolite:0x00007f5a88025758>

PDB for #<Metabolite:0x00007f5a88025758>

3D PDB for #<Metabolite:0x00007f5a88025758>

SMILES for #<Metabolite:0x00007f5a88025758>

INCHI for #<Metabolite:0x00007f5a88025758>

Structure for #<Metabolite:0x00007f5a88025758>

3D Structure for #<Metabolite:0x00007f5a88025758>