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Showing metabocard for Nitromethane (HMDB0255654)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 15:26:24 UTC
Update Date2021-09-26 23:10:40 UTC
HMDB IDHMDB0255654
Secondary Accession NumbersNone
Metabolite Identification
Common NameNitromethane
Descriptionnitromethane, also known as CH3NO2 or MENO2, belongs to the class of organic compounds known as c-nitro compounds. C-nitro compounds are compounds having the nitro group, -NO2 (free valence on nitrogen), which is attached to carbon. It is also used as a fuel for rockets and radio-controlled models. nitromethane is a very weakly acidic compound (based on its pKa). nitromethane is a potentially toxic compound. A polar solvent (b.p. 101 degreeC), it is an important starting material in organic synthesis. A primary nitroalkane that is methane in which one of the hydrogens is replace by a nitro group. This compound has been identified in human blood as reported by (PMID: 31557052 ). Nitromethane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Nitromethane 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 HMDB0255654 (Nitromethane)


  Mrv0541 08291401542D          

  4  3  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  2  0  0  0  0
M  END
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3D MOL for HMDB0255654 (Nitromethane)

HMDB0255654
     RDKit          3D
Nitromethane
  7  6  0  0  0  0  0  0  0  0999 V2000
   -0.6298   -0.1055    0.0119 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7961    0.0043    0.0129 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.5912   -0.9525    0.0216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3389    1.2786    0.0034 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0329    0.6825   -0.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0140   -1.0640   -0.3669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0494    0.1565    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
M  CHG  2   2   1   4  -1
M  END
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3D SDF for HMDB0255654 (Nitromethane)


  Mrv0541 08291401542D          

  4  3  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255654

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH3NO2/c1-2(3)4/h1H3

> <INCHI_KEY>
LYGJENNIWJXYER-UHFFFAOYSA-N

> <FORMULA>
CH3NO2

> <MOLECULAR_WEIGHT>
61.04

> <EXACT_MASS>
61.016378345

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
4.662125890576118

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
nitromethane

> <ALOGPS_LOGP>
-0.17

> <JCHEM_LOGP>
0.019534642999999713

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.304119066367397

> <JCHEM_POLAR_SURFACE_AREA>
45.82

> <JCHEM_REFRACTIVITY>
12.5876

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nitromethane

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0255654 (Nitromethane)

HMDB0255654
     RDKit          3D
Nitromethane
  7  6  0  0  0  0  0  0  0  0999 V2000
   -0.6298   -0.1055    0.0119 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7961    0.0043    0.0129 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.5912   -0.9525    0.0216 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3389    1.2786    0.0034 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0329    0.6825   -0.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0140   -1.0640   -0.3669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0494    0.1565    1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
M  CHG  2   2   1   4  -1
M  END
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PDB for HMDB0255654 (Nitromethane)

HEADER    PROTEIN                                 29-AUG-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-AUG-14         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0255654 (Nitromethane)

COMPND    HMDB0255654
HETATM    1  C1  UNL     1      -0.630  -0.105   0.012  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.796   0.004   0.013  1.00  0.00           N1+
HETATM    3  O1  UNL     1       1.591  -0.952   0.022  1.00  0.00           O  
HETATM    4  O2  UNL     1       1.339   1.279   0.003  1.00  0.00           O1-
HETATM    5  H1  UNL     1      -1.033   0.683  -0.688  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.014  -1.064  -0.367  1.00  0.00           H  
HETATM    7  H3  UNL     1      -1.049   0.156   1.005  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    3    4
END
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SMILES for HMDB0255654 (Nitromethane)

CN(=O)=O
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INCHI for HMDB0255654 (Nitromethane)

InChI=1S/CH3NO2/c1-2(3)4/h1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
CH3NO2ChEBI
MeNO2ChEBI
Chemical FormulaCH3NO2
Average Molecular Weight61.04
Monoisotopic Molecular Weight61.016378345
IUPAC Namenitromethane
Traditional Namenitromethane
CAS Registry NumberNot Available
SMILES
CN(=O)=O
InChI Identifier
InChI=1S/CH3NO2/c1-2(3)4/h1H3
InChI KeyLYGJENNIWJXYER-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as c-nitro compounds. C-nitro compounds are compounds having the nitro group, -NO2 (free valence on nitrogen), which is attached to carbon.
KingdomOrganic compounds
Super ClassOrganic 1,3-dipolar compounds
ClassAllyl-type 1,3-dipolar organic compounds
Sub ClassOrganic nitro compounds
Direct ParentC-nitro compounds
Alternative Parents
Substituents
  • C-nitro compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic oxoazanium
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
Process
Naturally occurring process
Role
Biological roleIndustrial applicationIndirect biological role
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-0.17ALOGPS
logP0.02ChemAxon
logS-0.47ALOGPS
pKa (Strongest Acidic)8.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area45.82 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity12.59 m³·mol⁻¹ChemAxon
Polarizability4.66 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]+121.70630932474
DeepCCS[M-H]-119.28230932474
DeepCCS[M-2H]-155.51730932474
DeepCCS[M+Na]+129.94130932474
AllCCS[M+H]+108.432859911
AllCCS[M+H-H2O]+103.932859911
AllCCS[M+NH4]+112.632859911
AllCCS[M+Na]+113.832859911
AllCCS[M-H]-138.832859911
AllCCS[M+Na-2H]-145.632859911
AllCCS[M+HCOO]-153.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NitromethaneCN(=O)=O1143.1Standard polar33892256
NitromethaneCN(=O)=O472.8Standard non polar33892256
NitromethaneCN(=O)=O478.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nitromethane GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-0d8b42d155a313e28e542021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nitromethane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-01q9-9000000000-32858365cd408a36afd62014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 10V, Positive-QTOFsplash10-03di-9000000000-7a089d3db38875cf98b32016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 20V, Positive-QTOFsplash10-0002-9000000000-cfd7ce27b0ce4b9da6b82016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 40V, Positive-QTOFsplash10-0002-9000000000-ab01e0270ee193390caa2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 10V, Negative-QTOFsplash10-0006-9000000000-b4751f915d48f8c966d12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 20V, Negative-QTOFsplash10-0006-9000000000-26e47c35d9810cc948532016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitromethane 40V, Negative-QTOFsplash10-0006-9000000000-f6ddab701b27eb29052c2016-08-03Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C 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 NMR1H NMR Spectrum (1D, 200 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, 300 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, 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 NMR13C NMR Spectrum (1D, 500 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 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 NMR1H NMR Spectrum (1D, 800 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, 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 IDNot Available
KEGG Compound IDC19275
BioCyc IDCPD-8133
BiGG IDNot Available
Wikipedia LinkNitromethane
METLIN IDNot Available
PubChem Compound6375
PDB IDNot Available
ChEBI ID77701
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 ]