Hmdb loader

Showing metabocard for Methylene (HMDB0249629)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...
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
Spectra
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 ]