Hmdb loader

Showing metabocard for Glycolaldehyde (HMDB0003344)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
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
Data?1676999796
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
Download

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
Download

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

$$$$
Download

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
Download

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
Download

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
Download

SMILES for HMDB0003344 (Glycolaldehyde)

OCC=O
Download

INCHI for HMDB0003344 (Glycolaldehyde)

InChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2
Download
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
PropertyValueSource
Water Solubility725 g/LALOGPS
logP-0.99ALOGPS
logP-1.2ChemAxon
logS1.08ALOGPS
pKa (Strongest Acidic)14.27ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity13.42 m³·mol⁻¹ChemAxon
Polarizability5.32 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+108.19631661259
DarkChem[M-H]-100.24831661259
DeepCCS[M+H]+120.38330932474
DeepCCS[M-H]-118.51130932474
DeepCCS[M-2H]-153.93830932474
DeepCCS[M+Na]+128.2930932474
AllCCS[M+H]+121.332859911
AllCCS[M+H-H2O]+116.832859911
AllCCS[M+NH4]+125.632859911
AllCCS[M+Na]+126.832859911
AllCCS[M-H]-139.832859911
AllCCS[M+Na-2H]-146.532859911
AllCCS[M+HCOO]-153.932859911

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, 2022.0.67 minutes32390414
Predicted by Siyang on May 30, 20228.1483 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.95 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid232.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid614.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid349.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid113.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid265.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid93.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid257.5 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 Acid283.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)331.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid551.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid57.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid726.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid228.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid295.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate622.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA301.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water268.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GlycolaldehydeOCC=O1268.5Standard polar33892256
GlycolaldehydeOCC=O520.6Standard non polar33892256
GlycolaldehydeOCC=O578.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Glycolaldehyde,1TMS,isomer #1C[Si](C)(C)OCC=O836.5Semi standard non polar33892256
Glycolaldehyde,1TMS,isomer #2C[Si](C)(C)OC=CO867.2Semi standard non polar33892256
Glycolaldehyde,2TMS,isomer #1C[Si](C)(C)OC=CO[Si](C)(C)C992.7Semi standard non polar33892256
Glycolaldehyde,2TMS,isomer #1C[Si](C)(C)OC=CO[Si](C)(C)C920.6Standard non polar33892256
Glycolaldehyde,2TMS,isomer #1C[Si](C)(C)OC=CO[Si](C)(C)C1010.2Standard polar33892256
Glycolaldehyde,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC=O1042.1Semi standard non polar33892256
Glycolaldehyde,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC=CO1085.5Semi standard non polar33892256
Glycolaldehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CO[Si](C)(C)C(C)(C)C1420.8Semi standard non polar33892256
Glycolaldehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CO[Si](C)(C)C(C)(C)C1384.2Standard non polar33892256
Glycolaldehyde,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC=CO[Si](C)(C)C(C)(C)C1321.4Standard polar33892256
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)Download (PDF)
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