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Showing metabocard for Glycolaldehyde (HMDB0003344)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-12 19:09:36 UTC
Update Date2023-02-21 17:16:36 UTC
HMDB IDHMDB0003344
Secondary Accession Numbers
  • HMDB0002165
  • HMDB02165
  • HMDB03344
Metabolite Identification
Common NameGlycolaldehyde
DescriptionGlycolaldehyde (HOCH2-CH=O, IUPAC name 2-hydroxyethanal) is a type of diose (2-carbon monosaccharide). Glycolaldehyde is readily converted to acetyl coenzyme A. It has an aldehyde and a hydroxyl group. However, it is not actually a sugar, because there is only one hydroxyl group. Glycolaldehyde is formed from many sources, including the amino acid glycine and from purone catabolism. It can form by action of ketolase on fructose 1,6-bisphosphate in an alternate glycolysis pathway. This compound is transferred by thiamin pyrophosphate during the pentose phosphate shunt.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003344 (Glycolaldehyde)

  Mrv1652309042000282D          

  4  3  0  0  0  0            999 V2000
   -2.1651    0.9036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8795    0.4910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4506    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7361    0.9036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for HMDB0003344 (Glycolaldehyde)

HMDB0003344
     RDKit          3D
Glycolaldehyde
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.7724    0.1823   -0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8799   -0.4703    0.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5062   -0.1415   -0.0626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5414    0.9064   -0.9742 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1476   -1.2452    1.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9330   -1.0661   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488    0.1020    0.8164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705    1.7324   -0.4509 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
M  END
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3D SDF for HMDB0003344 (Glycolaldehyde)

  Mrv1652309042000282D          

  4  3  0  0  0  0            999 V2000
   -2.1651    0.9036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8795    0.4910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4506    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7361    0.9036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003344

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2

> <INCHI_KEY>
WGCNASOHLSPBMP-UHFFFAOYSA-N

> <FORMULA>
C2H4O2

> <MOLECULAR_WEIGHT>
60.052

> <EXACT_MASS>
60.021129372

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
5.32025357658998

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxyacetaldehyde

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-1.1992100126666667

> <ALOGPS_LOGS>
1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.268537784266844

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1186437664146496

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
13.4205

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.25e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycolaldehyde

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003344 (Glycolaldehyde)

HMDB0003344
     RDKit          3D
Glycolaldehyde
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.7724    0.1823   -0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8799   -0.4703    0.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5062   -0.1415   -0.0626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5414    0.9064   -0.9742 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1476   -1.2452    1.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9330   -1.0661   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488    0.1020    0.8164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705    1.7324   -0.4509 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  3  6  1  0
  3  7  1  0
  4  8  1  0
M  END
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PDB for HMDB0003344 (Glycolaldehyde)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -4.041   1.687   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.375   0.917   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.708   0.917   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.374   1.687   0.000  0.00  0.00           O+0
CONECT    1    3    2                                                       
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0003344 (Glycolaldehyde)

COMPND    HMDB0003344
HETATM    1  O1  UNL     1       1.772   0.182  -0.161  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.880  -0.470   0.334  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.506  -0.141  -0.063  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.541   0.906  -0.974  1.00  0.00           O  
HETATM    5  H1  UNL     1       1.148  -1.245   1.027  1.00  0.00           H  
HETATM    6  H2  UNL     1      -0.933  -1.066  -0.528  1.00  0.00           H  
HETATM    7  H3  UNL     1      -1.149   0.102   0.816  1.00  0.00           H  
HETATM    8  H4  UNL     1      -0.671   1.732  -0.451  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    5
CONECT    3    4    6    7
CONECT    4    8
END
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SMILES for HMDB0003344 (Glycolaldehyde)

OCC=O
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INCHI for HMDB0003344 (Glycolaldehyde)

InChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
GLYCOALDEHYDEChEBI
Glycolic aldehydeChEBI
GlycollaldehydeChEBI
HydroxyacetaldehydeChEBI
Methylol formaldehydeChEBI
MonomethylolformaldehydeChEBI
2-HydroxyacetaldehydeHMDB
2-HydroxyethanalHMDB
2-OH-AcetaldehydeHMDB
2-OxoethanolHMDB
DioseHMDB
HydroxyethanalHMDB
MethylolformaldehydeHMDB
Chemical FormulaC2H4O2
Average Molecular Weight60.052
Monoisotopic Molecular Weight60.021129372
IUPAC Name2-hydroxyacetaldehyde
Traditional Nameglycolaldehyde
CAS Registry Number141-46-8
SMILES
OCC=O
InChI Identifier
InChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2
InChI KeyWGCNASOHLSPBMP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain aldehydes. These are an aldehyde with a chain length containing between 2 and 5 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentShort-chain aldehydes
Alternative Parents
Substituents
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point97 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Mitochondria
Biospecimen LocationsNot Available
Tissue Locations
  • Neuron
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030893
KNApSAcK IDC00007457
Chemspider ID736
KEGG Compound IDC00266
BioCyc IDGLYCOLALDEHYDE
BiGG ID34446
Wikipedia LinkGlycolaldehyde
METLIN ID3205
PubChem Compound756
PDB IDNot Available
ChEBI ID17071
Food Biomarker OntologyNot Available
VMH IDGCALD
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMajerski, Piotr A.; Piskorz, Jan K.; Radlein, Desmond St. A. G. Production of glycolaldehyde by hydrous thermolysis of sugars. PCT Int. Appl. (2002), 41 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Choei H, Sasaki N, Takeuchi M, Yoshida T, Ukai W, Yamagishi S, Kikuchi S, Saito T: Glyceraldehyde-derived advanced glycation end products in Alzheimer's disease. Acta Neuropathol. 2004 Sep;108(3):189-93. Epub 2004 Jun 17. [PubMed:15221334 ]
  2. Takeuchi M, Yamagishi S: TAGE (toxic AGEs) hypothesis in various chronic diseases. Med Hypotheses. 2004;63(3):449-52. [PubMed:15288366 ]

Enzymes

Enzyme Details
1. 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
Glycolaldehyde → (2-oxoethoxy)sulfonic aciddetails
Enzyme Details
2. 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
Glycolaldehyde → 3,4,5-trihydroxy-6-(2-oxoethoxy)oxane-2-carboxylic aciddetails