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Showing metabocard for Glycolic acid (HMDB0000115)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:31 UTC
HMDB IDHMDB0000115
Secondary Accession Numbers
  • HMDB0003035
  • HMDB00115
  • HMDB03035
Metabolite Identification
Common NameGlycolic acid
Description
Structure
Data?1676999671
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000115 (Glycolic acid)

  Mrv1652309032023522D          

  5  4  0  0  0  0            999 V2000
10000.894810001.0454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.609610000.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.325910001.0454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.179410000.6334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.894810001.8719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  3  1  0  0  0  0
M  END
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3D MOL for HMDB0000115 (Glycolic acid)

HMDB0000115
     RDKit          3D
Glycolic acid
  9  8  0  0  0  0  0  0  0  0999 V2000
    0.5818    1.6591    0.7826 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3893    0.5883    0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3180    0.0447   -0.6953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8817   -0.1396    0.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214   -1.2911   -0.3932 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3105    0.2603   -0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6969    0.5210   -0.0018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9694   -0.3392    1.4546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1303   -1.3035   -0.9892 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
  3  6  1  0
  4  7  1  0
  4  8  1  0
  5  9  1  0
M  END
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3D SDF for HMDB0000115 (Glycolic acid)

  Mrv1652309032023522D          

  5  4  0  0  0  0            999 V2000
10000.894810001.0454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.609610000.6334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.325910001.0454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.179410000.6334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.894810001.8719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000115

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H4O3/c3-1-2(4)5/h3H,1H2,(H,4,5)

> <INCHI_KEY>
AEMRFAOFKBGASW-UHFFFAOYSA-N

> <FORMULA>
C2H4O3

> <MOLECULAR_WEIGHT>
76.0514

> <EXACT_MASS>
76.016043994

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
6.195837007972227

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxyacetic acid

> <ALOGPS_LOGP>
-1.02

> <JCHEM_LOGP>
-1.0405937603333335

> <ALOGPS_LOGS>
0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.780077957574235

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.526322592592504

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6133096708862027

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
14.345899999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycolic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000115 (Glycolic acid)

HMDB0000115
     RDKit          3D
Glycolic acid
  9  8  0  0  0  0  0  0  0  0999 V2000
    0.5818    1.6591    0.7826 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3893    0.5883    0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3180    0.0447   -0.6953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8817   -0.1396    0.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9214   -1.2911   -0.3932 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3105    0.2603   -0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6969    0.5210   -0.0018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9694   -0.3392    1.4546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1303   -1.3035   -0.9892 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
  3  6  1  0
  4  7  1  0
  4  8  1  0
  5  9  1  0
M  END
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PDB for HMDB0000115 (Glycolic acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.3378668.618   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8669.6718667.849   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8671.0088668.618   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8667.0028667.849   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8668.3378670.161   0.000  0.00  0.00           O+0
CONECT    1    2    4    5                                                  
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0000115 (Glycolic acid)

COMPND    HMDB0000115
HETATM    1  O1  UNL     1       0.582   1.659   0.783  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.389   0.588   0.167  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.318   0.045  -0.695  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.882  -0.140   0.358  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.921  -1.291  -0.393  1.00  0.00           O  
HETATM    6  H1  UNL     1       2.311   0.260  -0.683  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.697   0.521  -0.002  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.969  -0.339   1.455  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.130  -1.304  -0.989  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    6
CONECT    4    5    7    8
CONECT    5    9
END
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SMILES for HMDB0000115 (Glycolic acid)

OCC(O)=O
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INCHI for HMDB0000115 (Glycolic acid)

InChI=1S/C2H4O3/c3-1-2(4)5/h3H,1H2,(H,4,5)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC2H4O3
Average Molecular Weight76.0514
Monoisotopic Molecular Weight76.016043994
IUPAC Name2-hydroxyacetic acid
Traditional Nameglycolic acid
CAS Registry Number79-14-1
SMILES
OCC(O)=O
InChI Identifier
InChI=1S/C2H4O3/c3-1-2(4)5/h3H,1H2,(H,4,5)
InChI KeyAEMRFAOFKBGASW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha hydroxy acids and derivatives. These are organic compounds containing a carboxylic acid substituted with a hydroxyl group on the adjacent carbon.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassAlpha hydroxy acids and derivatives
Direct ParentAlpha hydroxy acids and derivatives
Alternative Parents
Substituents
  • Alpha-hydroxy acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological roleIndirect biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point75 - 80 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.11HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Mitochondria
  • Peroxisome
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Sweat
  • Urine
Tissue Locations
  • Bladder
  • Epidermis
  • Fibroblasts
  • Liver
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Ethylene glycol poisoning
  1. Jacobsen D, Hewlett TP, Webb R, Brown ST, Ordinario AT, McMartin KE: Ethylene glycol intoxication: evaluation of kinetics and crystalluria. Am J Med. 1988 Jan;84(1):145-52. [PubMed:3337119 ]
Hemodialysis
  1. Ogawa Y, Machida N, Jahana M, Gakiya M, Chinen Y, Oda M, Morozumi M, Sugaya K: Major factors modulating the serum oxalic acid level in hemodialysis patients. Front Biosci. 2004 Sep 1;9:2901-8. [PubMed:15353324 ]
Branched-chain Keto Acid Dehydrogenase Kinase Deficiency
  1. Novarino G, El-Fishawy P, Kayserili H, Meguid NA, Scott EM, Schroth J, Silhavy JL, Kara M, Khalil RO, Ben-Omran T, Ercan-Sencicek AG, Hashish AF, Sanders SJ, Gupta AR, Hashem HS, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris RA, State MW, Gleeson JG: Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. 2012 Oct 19;338(6105):394-7. doi: 10.1126/science.1224631. Epub 2012 Sep 6. [PubMed:22956686 ]
Transurethral resection of the prostate
  1. Perier C, Mahul P, Molliex S, Auboyer C, Frey J: Progressive changes in glycine and glycine derivatives in plasma and cerebrospinal fluid after transurethral prostatic resection. Clin Chem. 1990 Dec;36(12):2152-3. [PubMed:2253377 ]
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 ]
Lung Cancer
  1. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I: HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25. [PubMed:18953024 ]
Biliary atresia
  1. Nittono H, Obinata K, Nakatsu N, Watanabe T, Niijima S, Sasaki H, Arisaka O, Kato H, Yabuta K, Miyano T: Sulfated and nonsulfated bile acids in urine of patients with biliary atresia: analysis of bile acids by high-performance liquid chromatography. J Pediatr Gastroenterol Nutr. 1986 Jan;5(1):23-9. [PubMed:3944741 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
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 ]
Fumarase deficiency
  1. Bastug O, Kardas F, Ozturk MA, Halis H, Memur S, Korkmaz L, Tag Z, Gunes T: A rare cause of opistotonus; fumaric aciduria: The first case presentation in Turkey. Turk Pediatri Ars. 2014 Mar 1;49(1):74-6. doi: 10.5152/tpa.2014.442. eCollection 2014 Mar. [PubMed:26078636 ]
D-2-hydroxyglutaric aciduria
  1. Chalmers RA, Lawson AM, Watts RW, Tavill AS, Kamerling JP, Hey E, Ogilvie D: D-2-hydroxyglutaric aciduria: case report and biochemical studies. J Inherit Metab Dis. 1980;3(1):11-5. [PubMed:6774165 ]
Primary hyperoxaluria I
  1. Holmgren G, Hornstrom T, Johansson S, Samuelson G: Primary hyperoxaluria (glycolic acid variant): a clinical and genetical investigation of eight cases. Ups J Med Sci. 1978;83(1):65-70. [PubMed:705974 ]
Glycolic aciduria
  1. Coulter-Mackie MB, White CT, Lange D, et al. (2002). Primary Hyperoxaluria Type 1. 2002 Jun 19 [Updated 2014 Jul 17]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1283/. University of Washington, Seattle.
Glutaric acidemia type 2
  1. Chlebeck PT, Milliner DS, Smith LH: Long-term prognosis in primary hyperoxaluria type II (L-glyceric aciduria). Am J Kidney Dis. 1994 Feb;23(2):255-9. [PubMed:8311084 ]
Associated OMIM IDs
DrugBank IDDB03085
Phenol Explorer Compound IDNot Available
FooDB IDFDB003298
KNApSAcK IDC00007461
Chemspider ID737
KEGG Compound IDC03547
BioCyc IDGLYCOLLATE
BiGG ID34090
Wikipedia LinkGlycolic_acid
METLIN ID3219
PubChem Compound757
PDB IDNot Available
ChEBI ID17497
Food Biomarker OntologyNot Available
VMH IDGLYCLT
MarkerDB IDMDB00013417
Good Scents IDNot Available
References
Synthesis ReferenceWitzemann, Edgar J. Preparation of glycollic acid. Journal of the American Chemical Society (1917), 39 109-12.
Material Safety Data Sheet (MSDS)Download (PDF)
General References

Enzymes

Enzyme Details
1. Glucose-6-phosphate 1-dehydrogenase
General function:
Involved in glucose-6-phosphate dehydrogenase activity
Specific function:
Produces pentose sugars for nucleic acid synthesis and main producer of NADPH reducing power.
Gene Name:
G6PD
Uniprot ID:
P11413
Molecular weight:
62467.88
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Enzyme Details
2. Sulfotransferase family cytosolic 2B member 1
General function:
Involved in sulfotransferase activity
Specific function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol.
Gene Name:
SULT2B1
Uniprot ID:
O00204
Molecular weight:
39598.595
Reactions
Glycolic acid → 2-(sulfooxy)acetic aciddetails
Enzyme Details
3. 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
Glycolic acid + NADP → Glyoxylic acid + NADPHdetails
Glycolic acid + NADP → Glyoxylic acid + NADPH + Hydrogen Iondetails
Enzyme Details
4. Cytochrome P450 4A11
General function:
Involved in monooxygenase activity
Specific function:
Catalyzes the omega- and (omega-1)-hydroxylation of various fatty acids such as laurate, myristate and palmitate. Has little activity toward prostaglandins A1 and E1. Oxidizes arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE).
Gene Name:
CYP4A11
Uniprot ID:
Q02928
Molecular weight:
59347.31
Reactions
Fatty acid + Oxygen + Reduced flavoprotein → Glycolic acid + Oxidized flavoprotein + Waterdetails
Enzyme Details
5. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Glycolic acid → 6-(carboxymethoxy)-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
Glycolic acid → 3,4,5-trihydroxy-6-[(2-hydroxyacetyl)oxy]oxane-2-carboxylic aciddetails
Enzyme Details
6. Hydroxyacid oxidase 1
General function:
Involved in FMN binding
Specific function:
Has 2-hydroxyacid oxidase activity. Most active on the 2-carbon substrate glycolate, but is also active on 2-hydroxy fatty acids, with high activity towards 2-hydroxy palmitate and 2-hydroxy octanoate.
Gene Name:
HAO1
Uniprot ID:
Q9UJM8
Molecular weight:
40923.945
Reactions
Glycolic acid + Oxygen → Glyoxylic acid + Hydrogen peroxidedetails
Enzyme Details
7. Hydroxyacid oxidase 2
General function:
Involved in FMN binding
Specific function:
Catalyzes the oxidation of L-alpha-hydroxy acids as well as, more slowly, that of L-alpha-amino acids.
Gene Name:
HAO2
Uniprot ID:
Q9NYQ3
Molecular weight:
38838.35
Reactions
Glycolic acid + Oxygen → Glyoxylic acid + Hydrogen peroxidedetails
Enzyme Details
8. Phosphoglycolate phosphatase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PGP
Uniprot ID:
A6NDG6
Molecular weight:
34005.69
Reactions
Phosphoglycolic acid + Water → Glycolic acid + Phosphatedetails
Enzyme Details
9. Cytochrome P450 4A22
General function:
Involved in monooxygenase activity
Specific function:
Catalyzes the omega- and (omega-1)-hydroxylation of various fatty acids such as laurate and palmitate. Shows no activity towards arachidonic acid and prostaglandin A1. Lacks functional activity in the kidney and does not contribute to renal 20-hydroxyeicosatetraenoic acid (20-HETE) biosynthesis.
Gene Name:
CYP4A22
Uniprot ID:
Q5TCH4
Molecular weight:
59245.28
Reactions
Fatty acid + Oxygen + Reduced flavoprotein → Glycolic acid + Oxidized flavoprotein + Waterdetails