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Showing metabocard for Diazomethane (HMDB0251153)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:27:32 UTC
Update Date2021-09-26 23:03:00 UTC
HMDB IDHMDB0251153
Secondary Accession NumbersNone
Metabolite Identification
Common NameDiazomethane
Descriptiondiazomethane, also known as diazirine or acomethylene, belongs to the class of organic compounds known as diazo compounds. These are organic compounds having the divalent diazo group, =N+=N-, attached to a carbon atom. Based on a literature review a small amount of articles have been published on diazomethane. This compound has been identified in human blood as reported by (PMID: 31557052 ). Diazomethane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Diazomethane 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 HMDB0251153 (Diazomethane)


  Mrv0541 05031418472D          

  3  2  0  0  0  0            999 V2000
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  3  2  2  0  0  0  0
M  CHG  2   2  -1   3   1
M  END
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3D MOL for HMDB0251153 (Diazomethane)

HMDB0251153
     RDKit          3D
Diazomethane
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.5274    0.0027    0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7253   -0.0151    0.1670 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.9320   -0.0095   -0.1037 N   0  0  0  0  0  2  0  0  0  0  0  0
   -1.0879   -0.9261   -0.0433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0420    0.9481   -0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  1  4  1  0
  1  5  1  0
M  CHG  2   2   1   3  -1
M  END
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3D SDF for HMDB0251153 (Diazomethane)


  Mrv0541 05031418472D          

  3  2  0  0  0  0            999 V2000
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  3  2  2  0  0  0  0
M  CHG  2   2  -1   3   1
M  END
> <DATABASE_ID>
HMDB0251153

> <DATABASE_NAME>
hmdb

> <SMILES>
C=[N+]=[N-]

> <INCHI_IDENTIFIER>
InChI=1S/CH2N2/c1-3-2/h1H2

> <INCHI_KEY>
YXHKONLOYHBTNS-UHFFFAOYSA-N

> <FORMULA>
CH2N2

> <MOLECULAR_WEIGHT>
42.04

> <EXACT_MASS>
42.021798074

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
3.612023683501505

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
diazomethane

> <ALOGPS_LOGP>
0.25

> <JCHEM_LOGP>
-1.9753160408759456

> <ALOGPS_LOGS>
-0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.567383761395707

> <JCHEM_PKA_STRONGEST_BASIC>
-7.901218677892012

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
9.007

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.33e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diazomethane

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0251153 (Diazomethane)

HMDB0251153
     RDKit          3D
Diazomethane
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.5274    0.0027    0.0207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7253   -0.0151    0.1670 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.9320   -0.0095   -0.1037 N   0  0  0  0  0  2  0  0  0  0  0  0
   -1.0879   -0.9261   -0.0433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0420    0.9481   -0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  1  4  1  0
  1  5  1  0
M  CHG  2   2   1   3  -1
M  END
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PDB for HMDB0251153 (Diazomethane)

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N-1
HETATM    3  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
CONECT    1    3                                                            
CONECT    2    3                                                            
CONECT    3    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
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3D PDB for HMDB0251153 (Diazomethane)

COMPND    HMDB0251153
HETATM    1  C1  UNL     1      -0.527   0.003   0.021  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.725  -0.015   0.167  1.00  0.00           N1+
HETATM    3  N2  UNL     1       1.932  -0.010  -0.104  1.00  0.00           N1-
HETATM    4  H1  UNL     1      -1.088  -0.926  -0.043  1.00  0.00           H  
HETATM    5  H2  UNL     1      -1.042   0.948  -0.041  1.00  0.00           H  
CONECT    1    2    2    4    5
CONECT    2    3    3
END
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SMILES for HMDB0251153 (Diazomethane)

C=[N+]=[N-]
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INCHI for HMDB0251153 (Diazomethane)

InChI=1S/CH2N2/c1-3-2/h1H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
AcomethyleneChEBI
AzimethyleneChEBI
DiazirineChEBI
Diazonium methylideChEBI
EINECS 206-382-7ChEBI
Chemical FormulaCH2N2
Average Molecular Weight42.04
Monoisotopic Molecular Weight42.021798074
IUPAC Namediazomethane
Traditional Namediazomethane
CAS Registry NumberNot Available
SMILES
C=[N+]=[N-]
InChI Identifier
InChI=1S/CH2N2/c1-3-2/h1H2
InChI KeyYXHKONLOYHBTNS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diazo compounds. These are organic compounds having the divalent diazo group, =N+=N-, attached to a carbon atom.
KingdomOrganic compounds
Super ClassOrganic 1,3-dipolar compounds
ClassPropargyl-type 1,3-dipolar organic compounds
Sub ClassDiazo compounds
Direct ParentDiazo compounds
Alternative Parents
Substituents
  • Diazo compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • 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
logP0.25ALOGPS
logP-2ChemAxon
logS-0.5ALOGPS
pKa (Strongest Acidic)9.57ChemAxon
pKa (Strongest Basic)-7.9ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity9.01 m³·mol⁻¹ChemAxon
Polarizability3.61 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]+112.86830932474
DeepCCS[M-H]-111.04730932474
DeepCCS[M-2H]-146.50930932474
DeepCCS[M+Na]+120.7630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DiazomethaneC=[N+]=[N-]967.8Standard polar33892256
DiazomethaneC=[N+]=[N-]243.3Standard non polar33892256
DiazomethaneC=[N+]=[N-]459.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Diazomethane GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9000000000-adae53adf9fd155a1b032021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Diazomethane 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 - Diazomethane 10V, Positive-QTOFsplash10-0006-9000000000-4a10346abbe8b1e787c22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diazomethane 20V, Positive-QTOFsplash10-0006-9000000000-b57ebfd696db899864012016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diazomethane 40V, Positive-QTOFsplash10-0006-9000000000-0efa4b84f5d49fb5b1d62016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diazomethane 10V, Negative-QTOFsplash10-004i-9000000000-2d8e2b790ad274c79ca52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diazomethane 20V, Negative-QTOFsplash10-004i-9000000000-4b75e30fcf46244091f72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Diazomethane 40V, Negative-QTOFsplash10-004i-9000000000-bab4dfade106801fa61b2016-08-03Wishart 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 ID9176
KEGG Compound IDC19387
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiazomethane
METLIN IDNot Available
PubChem Compound9550
PDB IDNot Available
ChEBI ID73716
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 ]