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Showing metabocard for Methanediol (HMDB0254518)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:51:18 UTC
Update Date2021-09-26 23:08:34 UTC
HMDB IDHMDB0254518
Secondary Accession NumbersNone
Metabolite Identification
Common NameMethanediol
Descriptionmethanediol, also known as methylene glycol or dihydroxymethane, belongs to the class of organic compounds known as carbonyl hydrates. These are organic compounds containing two hydroxyl groups attached to a carbon atom. Based on a literature review a significant number of articles have been published on methanediol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methanediol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methanediol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254518 (Methanediol)


  Mrv1533004251504312D          

  3  2  0  0  0  0            999 V2000
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  END
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3D MOL for HMDB0254518 (Methanediol)

HMDB0254518
     RDKit          3D
Methanediol
  7  6  0  0  0  0  0  0  0  0999 V2000
   -1.1029    0.2992   -0.3637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017   -0.4721   -0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2060    0.1845   -0.2358 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1685    1.1420    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0736   -0.8759    1.0233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0324   -1.3790   -0.6739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1732    1.1014    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  2  5  1  0
  2  6  1  0
  3  7  1  0
M  END
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3D SDF for HMDB0254518 (Methanediol)


  Mrv1533004251504312D          

  3  2  0  0  0  0            999 V2000
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254518

> <DATABASE_NAME>
hmdb

> <SMILES>
OCO

> <INCHI_IDENTIFIER>
InChI=1S/CH4O2/c2-1-3/h2-3H,1H2

> <INCHI_KEY>
CKFGINPQOCXMAZ-UHFFFAOYSA-N

> <FORMULA>
CH4O2

> <MOLECULAR_WEIGHT>
48.041

> <EXACT_MASS>
48.021129369

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
4.242148317286496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methanediol

> <ALOGPS_LOGP>
-1.65

> <JCHEM_LOGP>
-1.0985781383333333

> <ALOGPS_LOGS>
1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.619378544550816

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.481529029773395

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3313086822736926

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
9.363100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.33e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylene glycol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0254518 (Methanediol)

HMDB0254518
     RDKit          3D
Methanediol
  7  6  0  0  0  0  0  0  0  0999 V2000
   -1.1029    0.2992   -0.3637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017   -0.4721   -0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2060    0.1845   -0.2358 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1685    1.1420    0.1287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0736   -0.8759    1.0233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0324   -1.3790   -0.6739 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1732    1.1014    0.1421 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  2  5  1  0
  2  6  1  0
  3  7  1  0
M  END
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PDB for HMDB0254518 (Methanediol)

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.977  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2                                                            
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
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3D PDB for HMDB0254518 (Methanediol)

COMPND    HMDB0254518
HETATM    1  O1  UNL     1      -1.103   0.299  -0.364  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.002  -0.472  -0.021  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.206   0.184  -0.236  1.00  0.00           O  
HETATM    4  H1  UNL     1      -1.168   1.142   0.129  1.00  0.00           H  
HETATM    5  H2  UNL     1      -0.074  -0.876   1.023  1.00  0.00           H  
HETATM    6  H3  UNL     1      -0.032  -1.379  -0.674  1.00  0.00           H  
HETATM    7  H4  UNL     1       1.173   1.101   0.142  1.00  0.00           H  
CONECT    1    2    4
CONECT    2    3    5    6
CONECT    3    7
END
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SMILES for HMDB0254518 (Methanediol)

OCO
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INCHI for HMDB0254518 (Methanediol)

InChI=1S/CH4O2/c2-1-3/h2-3H,1H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
DihydroxymethaneChEBI
Formaldehyde hydrateChEBI
MethandiolChEBI
Methylene glycolChEBI
Formaldehyde hydric acidGenerator
Chemical FormulaCH4O2
Average Molecular Weight48.041
Monoisotopic Molecular Weight48.021129369
IUPAC Namemethanediol
Traditional Namemethylene glycol
CAS Registry NumberNot Available
SMILES
OCO
InChI Identifier
InChI=1S/CH4O2/c2-1-3/h2-3H,1H2
InChI KeyCKFGINPQOCXMAZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carbonyl hydrates. These are organic compounds containing two hydroxyl groups attached to a carbon atom.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentCarbonyl hydrates
Alternative Parents
Substituents
  • Carbonyl hydrate
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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-1.6ALOGPS
logP-1.1ChemAxon
logS1.29ALOGPS
pKa (Strongest Acidic)13.48ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity9.36 m³·mol⁻¹ChemAxon
Polarizability4.24 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+113.75430932474
DeepCCS[M-H]-111.95630932474
DeepCCS[M-2H]-147.22430932474
DeepCCS[M+Na]+120.8230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethanediolOCO1597.2Standard polar33892256
MethanediolOCO572.8Standard non polar33892256
MethanediolOCO612.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-ed209044154e0dd955e32021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methanediol GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID71348
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethanediol
METLIN IDNot Available
PubChem Compound79015
PDB IDNot Available
ChEBI ID48397
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1685111
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]