Hmdb loader

Showing metabocard for Glyoxal (HMDB0303107)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 23:22:21 UTC
Update Date2021-09-23 23:22:21 UTC
HMDB IDHMDB0303107
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlyoxal
DescriptionGlyoxal, also known as 1,2-ethanedione or oxalaldehyde, is a member of the class of compounds known as short-chain aldehydes. Short-chain aldehydes are an aldehyde with a chain length containing between 2 and 5 carbon atoms. Glyoxal is soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Glyoxal can be found in garden tomato (variety), ginger, and sesame, which makes glyoxal a potential biomarker for the consumption of these food products. Glyoxal is an organic compound with the chemical formula OCHCHO. It is a yellow-colored Liquid that evaporates to give a green-colored gas. Glyoxal is the smallest dialdehyde (two aldehyde groups). Its structure is more complicated than typically represented because the molecule hydrates and oligomerizes. It is produced industrially as a precursor to many products .
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303107 (Glyoxal)


  Mrv0541 02241221452D          

  4  3  0  0  0  0            999 V2000
    0.1105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
M  END
Download

3D MOL for HMDB0303107 (Glyoxal)

HMDB0303107
     RDKit          3D
Glyoxal
  6  5  0  0  0  0  0  0  0  0999 V2000
   -1.1520    0.1929   -1.2628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7072   -0.1112   -0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6926    0.1086    0.1330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1595   -0.1923    1.2663 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3090   -0.5283    0.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3162    0.5304   -0.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  2  5  1  0
  3  6  1  0
M  END
Download

3D SDF for HMDB0303107 (Glyoxal)


  Mrv0541 02241221452D          

  4  3  0  0  0  0            999 V2000
    0.1105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303107

> <DATABASE_NAME>
hmdb

> <SMILES>
O=CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H2O2/c3-1-2-4/h1-2H

> <INCHI_KEY>
LEQAOMBKQFMDFZ-UHFFFAOYSA-N

> <FORMULA>
C2H2O2

> <MOLECULAR_WEIGHT>
58.0361

> <EXACT_MASS>
58.005479308

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
4.502912633244565

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
oxaldehyde

> <ALOGPS_LOGP>
-0.04

> <JCHEM_LOGP>
-0.003598507333333334

> <ALOGPS_LOGS>
0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.771710838961624

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
12.561399999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.18e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glyoxal

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0303107 (Glyoxal)

HMDB0303107
     RDKit          3D
Glyoxal
  6  5  0  0  0  0  0  0  0  0999 V2000
   -1.1520    0.1929   -1.2628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7072   -0.1112   -0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6926    0.1086    0.1330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1595   -0.1923    1.2663 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3090   -0.5283    0.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3162    0.5304   -0.6513 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  2  5  1  0
  3  6  1  0
M  END
Download

PDB for HMDB0303107 (Glyoxal)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       0.206   0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.207   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
Download

3D PDB for HMDB0303107 (Glyoxal)

COMPND    HMDB0303107
HETATM    1  O1  UNL     1      -1.152   0.193  -1.263  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.707  -0.111  -0.135  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.693   0.109   0.133  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.160  -0.192   1.266  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.309  -0.528   0.650  1.00  0.00           H  
HETATM    6  H2  UNL     1       1.316   0.530  -0.651  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    5
CONECT    3    4    4    6
END
Download

SMILES for HMDB0303107 (Glyoxal)

O=CC=O
Download

INCHI for HMDB0303107 (Glyoxal)

InChI=1S/C2H2O2/c3-1-2-4/h1-2H
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2-EthanedioneChEBI
BiformalChEBI
BiformylChEBI
DiformalChEBI
DiformylChEBI
Ethane-1,2-dialChEBI
EthanedialChEBI
Glyoxal aldehydeChEBI
GlyoxylaldehydeChEBI
OxalChEBI
OxalaldehydeChEBI
EthanedioneMeSH
Chemical FormulaC2H2O2
Average Molecular Weight58.0361
Monoisotopic Molecular Weight58.005479308
IUPAC Nameoxaldehyde
Traditional Nameglyoxal
CAS Registry NumberNot Available
SMILES
O=CC=O
InChI Identifier
InChI=1S/C2H2O2/c3-1-2-4/h1-2H
InChI KeyLEQAOMBKQFMDFZ-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
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.04ALOGPS
logP-0.0036ChemAxon
logS0.57ALOGPS
pKa (Strongest Basic)-7.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity12.56 m³·mol⁻¹ChemAxon
Polarizability4.5 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
DeepCCS[M+H]+118.31930932474
DeepCCS[M-H]-116.41430932474
DeepCCS[M-2H]-152.09230932474
DeepCCS[M+Na]+126.49830932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 10V, Positive-QTOFsplash10-0a4i-9000000000-5f227adb81db17a036322016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 20V, Positive-QTOFsplash10-0a4i-9000000000-5f227adb81db17a036322016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 40V, Positive-QTOFsplash10-0a4i-9000000000-5f227adb81db17a036322016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 10V, Negative-QTOFsplash10-0a4i-9000000000-7bf79471a1bc3bbe478b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 20V, Negative-QTOFsplash10-0a4i-9000000000-7bf79471a1bc3bbe478b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 40V, Negative-QTOFsplash10-0a4i-9000000000-7bf79471a1bc3bbe478b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 10V, Positive-QTOFsplash10-0006-9000000000-c2ab8dab61a5f3adfdcb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 20V, Positive-QTOFsplash10-0006-9000000000-8d6ae997cbc4c4b575632021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 40V, Positive-QTOFsplash10-0006-9000000000-5ad321dbbf216c2775912021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 10V, Negative-QTOFsplash10-0a4i-9000000000-bd111b9d882611c30c682021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 20V, Negative-QTOFsplash10-0a4i-9000000000-bd111b9d882611c30c682021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Glyoxal 40V, Negative-QTOFsplash10-0a4i-9000000000-bd111b9d882611c30c682021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
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 IDFDB007802
KNApSAcK IDC00000211
Chemspider ID7572
KEGG Compound IDC14448
BioCyc IDCPD-8887
BiGG IDNot Available
Wikipedia LinkGlyoxal
METLIN IDNot Available
PubChem Compound7860
PDB IDNot Available
ChEBI ID34779
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1248641
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available