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Showing metabocard for Glyceric acid (HMDB0000139)

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enzymes (8) Show 8 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:58 UTC
HMDB IDHMDB0000139
Secondary Accession Numbers
  • HMDB00139
  • HMDB0031818
Metabolite Identification
Common NameGlyceric acid
DescriptionGlyceric 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
Data?1676999673
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000139 (Glyceric acid)

      
  Mrv1652309032023542D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5939 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000139 (Glyceric acid)

HMDB0000139
     RDKit          3D
Glyceric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.7473    0.4350    2.2873 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9500    0.2125    1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0845   -0.4463    0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0365    0.6630    0.0767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1107    1.3055    0.6709 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -0.5298   -0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.4505    0.0629 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5674   -0.2581   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4397    1.3811   -0.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    1.8640   -0.0319 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0275   -1.1260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1498   -0.2275   -1.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820   -1.9214   -0.5067 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  3  8  1  0
  4  9  1  6
  5 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
M  END
Download

3D SDF for HMDB0000139 (Glyceric acid)

      
  Mrv1652309032023542D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5939 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000139

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C3H6O4

> <MOLECULAR_WEIGHT>
106.0773

> <EXACT_MASS>
106.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.95589682155052

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,3-dihydroxypropanoic acid

> <ALOGPS_LOGP>
-1.72

> <JCHEM_LOGP>
-1.5187394846666669

> <ALOGPS_LOGS>
0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.495349861440904

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4186061267841343

> <JCHEM_PKA_STRONGEST_BASIC>
-3.042760876836586

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
20.383499999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycerate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000139 (Glyceric acid)

HMDB0000139
     RDKit          3D
Glyceric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.7473    0.4350    2.2873 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9500    0.2125    1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0845   -0.4463    0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0365    0.6630    0.0767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1107    1.3055    0.6709 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -0.5298   -0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.4505    0.0629 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5674   -0.2581   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4397    1.3811   -0.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    1.8640   -0.0319 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0275   -1.1260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1498   -0.2275   -1.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820   -1.9214   -0.5067 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  3  8  1  0
  4  9  1  6
  5 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
M  END
Download

PDB for HMDB0000139 (Glyceric acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0    8666.7108666.291   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8665.3768667.061   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8664.0428666.291   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8665.3768668.601   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8668.0448667.061   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8669.3848666.291   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8666.7108664.751   0.000  0.00  0.00           O+0
CONECT    1    2    5    7                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5                                                            
CONECT    7    1                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0000139 (Glyceric acid)

COMPND    HMDB0000139
HETATM    1  O1  UNL     1       0.747   0.435   2.287  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.950   0.213   1.063  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.084  -0.446   0.653  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.036   0.663   0.077  1.00  0.00           C  
HETATM    5  O3  UNL     1      -1.111   1.306   0.671  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.469  -0.530  -0.747  1.00  0.00           C  
HETATM    7  O4  UNL     1      -1.123  -1.451   0.063  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.567  -0.258  -0.220  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.440   1.381  -0.611  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.562   1.864  -0.032  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.444  -1.028  -1.126  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.150  -0.228  -1.570  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.782  -1.921  -0.507  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    8
CONECT    4    5    6    9
CONECT    5   10
CONECT    6    7   11   12
CONECT    7   13
END
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SMILES for HMDB0000139 (Glyceric acid)

OC[C@@H](O)C(O)=O
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INCHI for HMDB0000139 (Glyceric acid)

InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
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 Weight106.0773
Monoisotopic Molecular Weight106.02660868
IUPAC Name(2R)-2,3-dihydroxypropanoic acid
Traditional Nameglycerate
CAS Registry Number473-81-4
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 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 effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available113.3http://allccs.zhulab.cn/database/detail?ID=AllCCS00002116
Predicted Molecular Properties
PropertyValueSource
Water Solubility639 g/LALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+120.36731661259
DarkChem[M-H]-114.4431661259
AllCCS[M+H]+127.98132859911
AllCCS[M-H]-120.732859911
DeepCCS[M+H]+118.36330932474
DeepCCS[M-H]-115.56230932474
DeepCCS[M-2H]-152.02930932474
DeepCCS[M+Na]+126.73230932474
AllCCS[M+H]+128.032859911
AllCCS[M+H-H2O]+123.732859911
AllCCS[M+NH4]+132.032859911
AllCCS[M+Na]+133.132859911
AllCCS[M-H]-120.732859911
AllCCS[M+Na-2H]-124.532859911
AllCCS[M+HCOO]-128.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.1 minutes32390414
Predicted by Siyang on May 30, 20229.4345 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.02 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid290.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid711.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid374.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid53.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid252.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid107.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid289.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid250.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)615.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid605.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid47.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid814.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid226.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid308.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate713.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA314.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water366.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Glyceric acidOC[C@@H](O)C(O)=O2227.6Standard polar33892256
Glyceric acidOC[C@@H](O)C(O)=O1044.9Standard non polar33892256
Glyceric acidOC[C@@H](O)C(O)=O1100.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Glyceric acid,1TMS,isomer #1C[Si](C)(C)OC[C@@H](O)C(=O)O1155.8Semi standard non polar33892256
Glyceric acid,1TMS,isomer #2C[Si](C)(C)O[C@H](CO)C(=O)O1189.2Semi standard non polar33892256
Glyceric acid,1TMS,isomer #3C[Si](C)(C)OC(=O)[C@H](O)CO1085.5Semi standard non polar33892256
Glyceric acid,2TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)C(=O)O1258.6Semi standard non polar33892256
Glyceric acid,2TMS,isomer #2C[Si](C)(C)OC[C@@H](O)C(=O)O[Si](C)(C)C1223.2Semi standard non polar33892256
Glyceric acid,2TMS,isomer #3C[Si](C)(C)OC(=O)[C@@H](CO)O[Si](C)(C)C1220.3Semi standard non polar33892256
Glyceric acid,3TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C1328.0Semi standard non polar33892256
Glyceric acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O)C(=O)O1419.6Semi standard non polar33892256
Glyceric acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H](CO)C(=O)O1442.1Semi standard non polar33892256
Glyceric acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@H](O)CO1338.7Semi standard non polar33892256
Glyceric acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O1703.4Semi standard non polar33892256
Glyceric acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C1658.5Semi standard non polar33892256
Glyceric acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CO)O[Si](C)(C)C(C)(C)C1675.1Semi standard non polar33892256
Glyceric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1960.9Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Sweat
  • Urine
Tissue Locations
  • Placenta
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Female
Normal		 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Female
Normal		 details
BloodDetected and Quantified<5 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified10.0 (0.0-24.0) uMAdult (>18 years old)BothNormal details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified34.0+/- 34.0 uMAdult (>18 years old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified8.20 +/- 3.95 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
SweatDetected but not QuantifiedNot QuantifiedAdult BothNormal details
UrineDetected and Quantified3.18 (1.06-7.97) umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • Analysis of 40 NI...
 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected and Quantified0-0.9 umol/mmol creatinineInfant (0-1 year old)Male
Normal		 details
UrineDetected and Quantified0-2 umol/mmol creatinineInfant (0-1 year old)Female
Normal		 details
UrineDetected and Quantified4.1 umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified1.0-1.8 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified1.5-2.1 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified61.247 +/- 35.4 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified15.9 (7.8-31.1) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified14.4 (7.8-28.8) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified1.7 (0.2-6.0) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified3.5 (0.1-8.0) umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified5.3 (0.1-37.3) umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified8.9 (2.4-60.0) umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified21.6 (0.5-91.1) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified3.5 (2.8 - 4.2) umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified18.9 umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified20.4 umol/mmol creatinineInfant (0-1 year old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Schizophrenia		 details
BloodDetected and Quantified186-315 uMChildren (1-13 years old)BothD-Glyceric acidura details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Irritable bowel syndrome		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn disease		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
UrineDetected and Quantified2360.0 (1.2 - 1450.0) umol/mmol creatinineAdult (>18 years old)BothPrimary Hyperoxaluria II, PH2 details
UrineDetected and Quantified15000.0 (10000.0-20000.0) umol/mmol creatinineChildren (1-13 years old)BothD-Glyceric acidura
    • MetaGene: Metabol...
 details
UrineDetected and Quantified85.303 +/- 85.515 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 details
UrineDetected and Quantified2900-5220 umol/mmol creatinineChildren (1-13 years old)BothD-Glyceric acidura details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
Schizophrenia
  1. Yang J, Chen T, Sun L, Zhao Z, Qi X, Zhou K, Cao Y, Wang X, Qiu Y, Su M, Zhao A, Wang P, Yang P, Wu J, Feng G, He L, Jia W, Wan C: Potential metabolite markers of schizophrenia. Mol Psychiatry. 2013 Jan;18(1):67-78. doi: 10.1038/mp.2011.131. Epub 2011 Oct 25. [PubMed:22024767 ]
Irritable bowel syndrome
  1. Ponnusamy K, Choi JN, Kim J, Lee SY, Lee CH: Microbial community and metabolomic comparison of irritable bowel syndrome faeces. J Med Microbiol. 2011 Jun;60(Pt 6):817-27. doi: 10.1099/jmm.0.028126-0. Epub 2011 Feb 17. [PubMed:21330412 ]
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Crohn's disease
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Ulcerative colitis
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Primary hyperoxaluria
  1. 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 ]
Primary hyperoxaluria II
  1. 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 ]
  2. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
D-Glyceric acidura
  1. Bonham JR, Stephenson TJ, Carpenter KH, Rattenbury JM, Cromby CH, Pollitt RJ, Hull D: D(+)-glyceric aciduria: etiology and clinical consequences. Pediatr Res. 1990 Jul;28(1):38-41. [PubMed:2165585 ]
  2. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
D-Glyceric acidemia
  1. Bonham JR, Stephenson TJ, Carpenter KH, Rattenbury JM, Cromby CH, Pollitt RJ, Hull D: D(+)-glyceric aciduria: etiology and clinical consequences. Pediatr Res. 1990 Jul;28(1):38-41. [PubMed:2165585 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012242
KNApSAcK IDC00001185
Chemspider ID388334
KEGG Compound IDC00258
BioCyc IDGLYCERATE
BiGG ID34424
Wikipedia LinkGlyceric acid
METLIN ID280
PubChem Compound439194
PDB IDNot Available
ChEBI ID32398
Food Biomarker OntologyNot Available
VMH IDGLYC_R
MarkerDB IDMDB00000067
Good Scents IDNot Available
References
Synthesis ReferenceKyriacou, 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)Download (PDF)
General References
  1. 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 ]
  2. 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. [PubMed:14708889 ]
  3. 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 ]
  4. 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. [PubMed:8412012 ]
  5. 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 ]
  6. 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. [PubMed:11930278 ]
  7. 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 ]
  8. 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. [PubMed:1444166 ]
  9. 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. [PubMed:11920944 ]
  10. 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 ]
  11. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. 4-trimethylaminobutyraldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Converts gamma-trimethylaminobutyraldehyde into gamma-butyrobetaine. Catalyzes the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction.
Gene Name:
ALDH9A1
Uniprot ID:
P49189
Molecular weight:
56291.485
Reactions
Glyceraldehyde + NAD + Water → Glyceric acid + NADH + Hydrogen Iondetails
Enzyme Details
2. Alpha-aminoadipic semialdehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Multifunctional enzyme mediating important protective effects. Metabolizes betaine aldehyde to betaine, an important cellular osmolyte and methyl donor. Protects cells from oxidative stress by metabolizing a number of lipid peroxidation-derived aldehydes. Involved in lysine catabolism.
Gene Name:
ALDH7A1
Uniprot ID:
P49419
Molecular weight:
58486.74
Reactions
Glyceraldehyde + NAD + Water → Glyceric acid + NADH + Hydrogen Iondetails
Enzyme Details
3. Aldehyde dehydrogenase family 1 member A3
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Seems to be the key enzyme in the formation of an RA gradient along the dorso-ventral axis during the early eye development and also in the development of the olfactory system (By similarity).
Gene Name:
ALDH1A3
Uniprot ID:
P47895
Molecular weight:
56107.995
Enzyme Details
4. Aldehyde dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
ALDH2
Uniprot ID:
P05091
Molecular weight:
56380.93
Reactions
Glyceraldehyde + NAD + Water → Glyceric acid + NADH + Hydrogen Iondetails
Enzyme Details
5. Fatty aldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acids. Active on a variety of saturated and unsaturated aliphatic aldehydes between 6 and 24 carbons in length. Responsible for conversion of the sphingosine 1-phosphate (S1P) degradation product hexadecenal to hexadecenoic acid.
Gene Name:
ALDH3A2
Uniprot ID:
P51648
Molecular weight:
54847.36
Reactions
Glyceraldehyde + NAD + Water → Glyceric acid + NADH + Hydrogen Iondetails
Enzyme Details
6. Aldehyde dehydrogenase X, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
ALDHs play a major role in the detoxification of alcohol-derived acetaldehyde. They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation.
Gene Name:
ALDH1B1
Uniprot ID:
P30837
Molecular weight:
57248.96
Reactions
Glyceraldehyde + NAD + Water → Glyceric acid + NADH + Hydrogen Iondetails
Enzyme Details
7. Glyoxylate reductase/hydroxypyruvate reductase
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.
Gene Name:
GRHPR
Uniprot ID:
Q9UBQ7
Molecular weight:
35667.875
Reactions
Glyceric acid + NAD(P)(+) → Hydroxypyruvic acid + NAD(P)Hdetails
Glyceric acid + NAD → Hydroxypyruvic acid + NADH + Hydrogen Iondetails
Glyceric acid + NADP → Hydroxypyruvic acid + NADPH + Hydrogen Iondetails
Enzyme Details
8. Glycerate kinase
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
GLYCTK
Uniprot ID:
Q8IVS8
Molecular weight:
25036.865
Reactions
Adenosine triphosphate + Glyceric acid → ADP + 3-Phosphoglyceric aciddetails