Hmdb loader

Showing metabocard for Methylene (HMDB0249629)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 06:20:00 UTC
Update Date2021-09-26 23:00:38 UTC
HMDB IDHMDB0249629
Secondary Accession NumbersNone
Metabolite Identification
Common NameMethylene
DescriptionMethylene, also known as carbene or CH2(2.), belongs to the class of organic compounds known as saturated hydrocarbons. These are hydrocarbons that contains only saturated carbon atoms, which are linked to one another through single bonds. These includes alkanes and cycloalkanes. In humans, methylene is involved in the glycine and serine metabolism pathway. Methylene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Methylene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methylene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methylene 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0249629 (Methylene)


  Mrv1652309112108202D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
M  RAD  1   1   1
M  END
Download

3D MOL for HMDB0249629 (Methylene)

HMDB0249629
     RDKit          3D
Methylene
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0043    0.4404   -0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -0.8927   -0.2219   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8970   -0.2186    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  RAD  1   1   3
M  END
Download

3D SDF for HMDB0249629 (Methylene)


  Mrv1652309112108202D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
M  RAD  1   1   1
M  END
> <DATABASE_ID>
HMDB0249629

> <DATABASE_NAME>
hmdb

> <SMILES>
[CH2]

> <INCHI_IDENTIFIER>
InChI=1S/CH2/h1H2

> <INCHI_KEY>
HZVOZRGWRWCICA-UHFFFAOYSA-N

> <FORMULA>
CH2

> <MOLECULAR_WEIGHT>
14.027

> <EXACT_MASS>
14.015650064

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
1.9718292734736367

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methylidene

> <ALOGPS_LOGP>
-1.31

> <JCHEM_LOGP>
0.6322

> <ALOGPS_LOGS>
1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
3.701

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
0.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylidene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0249629 (Methylene)

HMDB0249629
     RDKit          3D
Methylene
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0043    0.4404   -0.0000 C   0  0  0  0  0  2  0  0  0  0  0  0
   -0.8927   -0.2219   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8970   -0.2186    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  RAD  1   1   3
M  END
Download

PDB for HMDB0249629 (Methylene)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0249629 (Methylene)

COMPND    HMDB0249629
HETATM    1  C1  UNL     1      -0.004   0.440  -0.000  1.00  0.00           C  
HETATM    2  H1  UNL     1      -0.893  -0.222  -0.000  1.00  0.00           H  
HETATM    3  H2  UNL     1       0.897  -0.219   0.000  1.00  0.00           H  
CONECT    1    2    3
END
Download

SMILES for HMDB0249629 (Methylene)

[CH2]
Download

INCHI for HMDB0249629 (Methylene)

InChI=1S/CH2/h1H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
CH2(2.)ChEBI
Methylene radicalChEBI
CarbeneHMDB
Carbene ion (-1)HMDB
Carbene, 13C-labeledHMDB
DimethoxycarbeneHMDB
MethyleneChEBI
Chemical FormulaCH2
Average Molecular Weight14.027
Monoisotopic Molecular Weight14.015650064
IUPAC Namemethylidene
Traditional Namemethylidene
CAS Registry NumberNot Available
SMILES
[CH2]
InChI Identifier
InChI=1S/CH2/h1H2
InChI KeyHZVOZRGWRWCICA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as saturated hydrocarbons. These are hydrocarbons that contains only saturated carbon atoms, which are linked to one another through single bonds. These includes alkanes and cycloalkanes.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassNot Available
Direct ParentSaturated hydrocarbons
Alternative Parents
Substituents
  • Saturated hydrocarbon
  • Carbene
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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-1.3ALOGPS
logP0.63ChemAxon
logS1.08ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity3.7 m³·mol⁻¹ChemAxon
Polarizability1.97 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]+112.17630932474
DeepCCS[M-H]-110.41530932474
DeepCCS[M-2H]-145.71730932474
DeepCCS[M+Na]+119.23130932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.3949 minutes33406817
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1033.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid458.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid201.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid370.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid216.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid352.5 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 Acid435.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)572.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid732.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid228.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid840.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid315.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid380.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate703.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA404.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water277.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methylene[CH2]246.9Standard polar33892256
Methylene[CH2]172.8Standard non polar33892256
Methylene[CH2]100.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Methylene GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-aa837ab5a5f1500bd0c22021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methylene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 10V, Positive-QTOFsplash10-014i-9000000000-a248014be23e776a6e982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 20V, Positive-QTOFsplash10-014i-9000000000-a248014be23e776a6e982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 40V, Positive-QTOFsplash10-014i-9000000000-a248014be23e776a6e982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 10V, Negative-QTOFsplash10-03di-9000000000-4ad1f92226f5696194af2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 20V, Negative-QTOFsplash10-03di-9000000000-4ad1f92226f5696194af2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylene 40V, Negative-QTOFsplash10-03di-9000000000-4ad1f92226f5696194af2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID109779
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethylene bridge
METLIN IDNot Available
PubChem Compound123164
PDB IDNot Available
ChEBI ID29357
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
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 ]