Human Metabolome Database Version 3.5

Showing metabocard for Glyceric acid (HMDB00139)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:07:57 -0700
HMDB ID HMDB00139
Secondary Accession Numbers None
Metabolite Identification
Common Name Glyceric acid
Description Glyceric acid is a colorless 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 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.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (R)-glycerate
  2. a,b-Hydroxypropionate
  3. a,b-Hydroxypropionic acid
  4. D-Glycerate
  5. D-Glyceric acid
  6. Glycerate
  7. Glyceric acid
Chemical Formula C3H6O4
Average Molecular Weight 106.0773
Monoisotopic Molecular Weight 106.02660868
IUPAC Name (2R)-2,3-dihydroxypropanoic acid
Traditional IUPAC Name glyceric acid
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
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Sugar Acids and Derivatives
Sub Class N/A
Other Descriptors
  • Aliphatic Acyclic Compounds
  • Beta Hydroxy Acids and Derivatives
  • trionic acid(ChEBI)
Substituents
  • 1,2 Diol
  • Alpha Hydroxy Acid
  • Carboxylic Acid
  • Primary Alcohol
  • Secondary Alcohol
  • Triose Monosaccharide
Direct Parent Sugar Acids and Derivatives
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
State Liquid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility 1000.0 mg/mL Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 639 g/L ALOGPS
LogP -1.72 ALOGPS
LogP -1.5 ChemAxon
LogS 0.78 ALOGPS
pKa (strongest acidic) 3.42 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 77.76 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 20.38 ChemAxon
Polarizability 8.96 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -1 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
MS/MS Spectrum GC-MS
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Prostate
Pathways
Name SMPDB Link KEGG Link
Glycine and Serine Metabolism SMP00004 map00260 Link_out
Glycerolipid Metabolism SMP00039 map00561 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
10.0 (0.0-24.0) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
<5 uM Adult (>18 years old) Not Specified Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
34.0+/- 34.0 uM Adult (>18 years old) Not Specified Normal
Urine Detected and Quantified
14.4 (7.8-28.8) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
21.6 (0.5-91.1) umol/mmol creatinine Newborn (0-30 days old) Both Normal
Urine Detected and Quantified
8.9 (2.4-60.0) umol/mmol creatinine Infant (0-1 year old) Both Normal
Urine Detected and Quantified
5.3 (0.1-37.3) umol/mmol creatinine Children (1-13 year old) Both Normal
Urine Detected and Quantified
3.5 (0.1-8.0) umol/mmol creatinine Children (1-13 year old) Both Normal
Urine Detected and Quantified
4.5 (0.00-9.0) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
15.9 (7.8-31.1) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
1.7 (0.2-6.0) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
4.1 umol/mmol creatinine Newborn (0-30 days old) Both Normal
Urine Detected and Quantified
20.4 umol/mmol creatinine Infant (0-1 year old) Both Normal
Urine Detected and Quantified
18.9 umol/mmol creatinine Infant (0-1 year old) Both Normal
Urine Detected and Quantified
3.5 (2.8 - 4.2) umol/mmol creatinine Adolescent (13-18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Urine Detected and Quantified 300.00 (150.00-450.00) umol/mmol creatinine Children (1-13 year old) Both Primary hyperoxaluria II
Urine Detected and Quantified 15000.0 (10000.0-20000.0) umol/mmol creatinine Children (1-13 year old) Both D-Glyceric acidura
Urine Detected and Quantified 2360.0 (1.2 - 1450.0) umol/mmol creatinine Adult (>18 years old) Both Primary Hyperoxaluria II, PH2
Associated Disorders and Diseases
Disease References
Primary hyperoxaluria
  • 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 Link_out
      D-Glyceric acidemia
          Primary hyperoxaluria II, PH2
              Associated OMIM IDs
              DrugBank ID Not Available
              DrugBank Metabolite ID Not Available
              Phenol Explorer Compound ID Not Available
              Phenol Explorer Metabolite ID Not Available
              FoodDB ID FDB012242
              KNApSAcK ID C00001185 Link_out
              Chemspider ID 388334 Link_out
              KEGG Compound ID C00258 Link_out
              BioCyc ID 2-PG Link_out
              BiGG ID 34424 Link_out
              Wikipedia Link Glyceric acid Link_out
              NuGOwiki Link HMDB00139 Link_out
              Metagene Link HMDB00139 Link_out
              METLIN ID 280 Link_out
              PubChem Compound 439194 Link_out
              PDB ID DGY Link_out
              ChEBI ID 32398 Link_out
              References
              Synthesis Reference Kyriacou, Demetrios; Tougas, Terrence P. Preparation of glyceric acid by anodic oxidation of glycerol at a silver oxide electrode. Journal of Organic Chemistry (1987), 52(11), 2318-19.
              Material Safety Data Sheet (MSDS) Download (PDF)
              General References
              1. 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 Link_out
              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 Link_out
              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 Link_out
              4. 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 Link_out
              5. 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 Link_out
              6. 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 Link_out
              7. 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 Link_out
              8. 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 Link_out
              9. 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. Pubmed: 19212411 Link_out

              Enzymes
              Name: 4-trimethylaminobutyraldehyde dehydrogenase
              Reactions:
              Glyceraldehyde + NAD + Water unknown Glyceric acid + NADH + Hydrogen Ion details
              Gene Name: ALDH9A1
              Uniprot ID: P49189 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Alpha-aminoadipic semialdehyde dehydrogenase
              Reactions:
              Glyceraldehyde + NAD + Water unknown Glyceric acid + NADH + Hydrogen Ion details
              Gene Name: ALDH7A1
              Uniprot ID: P49419 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Aldehyde dehydrogenase family 1 member A3
              Reactions: Not Available
              Gene Name: ALDH1A3
              Uniprot ID: P47895 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Aldehyde dehydrogenase, mitochondrial
              Reactions:
              Glyceraldehyde + NAD + Water unknown Glyceric acid + NADH + Hydrogen Ion details
              Gene Name: ALDH2
              Uniprot ID: P05091 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Fatty aldehyde dehydrogenase
              Reactions:
              Glyceraldehyde + NAD + Water unknown Glyceric acid + NADH + Hydrogen Ion details
              Gene Name: ALDH3A2
              Uniprot ID: P51648 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Aldehyde dehydrogenase X, mitochondrial
              Reactions:
              Glyceraldehyde + NAD + Water unknown Glyceric acid + NADH + Hydrogen Ion details
              Gene Name: ALDH1B1
              Uniprot ID: P30837 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Glyoxylate reductase/hydroxypyruvate reductase
              Reactions:
              Glyceric acid + NAD(P)(+) unknown Hydroxypyruvic acid + NAD(P)H details
              Glyceric acid + NAD unknown Hydroxypyruvic acid + NADH + Hydrogen Ion details
              Glyceric acid + NADP unknown Hydroxypyruvic acid + NADPH + Hydrogen Ion details
              Gene Name: GRHPR
              Uniprot ID: Q9UBQ7 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Glycerate kinase
              Reactions:
              Adenosine triphosphate + Glyceric acid unknown ADP + 3-Phosphoglyceric acid details
              Gene Name: GLYCTK
              Uniprot ID: Q8IVS8 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA