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Showing metabocard for 5,5-Dimethyl-1-pyrroline N-oxide (HMDB0246162)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:11:54 UTC
Update Date2021-09-26 22:55:03 UTC
HMDB IDHMDB0246162
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,5-Dimethyl-1-pyrroline N-oxide
Description5,5-Dimethyl-1-pyrroline N-oxide, also known as DMPO, belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms. Based on a literature review a significant number of articles have been published on 5,5-Dimethyl-1-pyrroline N-oxide. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5,5-dimethyl-1-pyrroline n-oxide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5,5-Dimethyl-1-pyrroline N-oxide 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 HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)


  Mrv1652309112101122D          

  8  8  0  0  0  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  CHG  2   6   1   7  -1
M  END
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3D MOL for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

HMDB0246162
     RDKit          3D
5,5-Dimethyl-1-pyrroline N-oxide
 19 19  0  0  0  0  0  0  0  0999 V2000
   -1.3453   -1.2068   -0.6261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4090   -0.1592   -0.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1722    0.6426    0.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8435   -0.7696    0.4848 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8300    0.3878    0.3643 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3024    1.0701   -0.8458 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0762    0.7555   -1.0518 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6772    1.2269   -2.0900 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.4028   -0.8859   -0.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2423   -2.0875    0.0739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -1.5597   -1.6177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2226    0.7410    0.6192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7363    1.6674    1.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2092    0.1819    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1337   -1.6108   -0.1923 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7673   -1.1427    1.5213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8523   -0.0089    0.2245 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7074    1.0158    1.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9347    1.7420   -1.4386 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
M  CHG  2   7   1   8  -1
M  END
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3D SDF for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)


  Mrv1652309112101122D          

  8  8  0  0  0  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
M  CHG  2   6   1   7  -1
M  END
> <DATABASE_ID>
HMDB0246162

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CCC=[N+]1[O-]

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO/c1-6(2)4-3-5-7(6)8/h5H,3-4H2,1-2H3

> <INCHI_KEY>
VCUVETGKTILCLC-UHFFFAOYSA-N

> <FORMULA>
C6H11NO

> <MOLECULAR_WEIGHT>
113.16

> <EXACT_MASS>
113.084063978

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.446892765109695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,2-dimethyl-3,4-dihydro-2H-pyrrol-1-ium-1-olate

> <ALOGPS_LOGP>
0.34

> <JCHEM_LOGP>
-2.6401102571384127

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.357824563531244

> <JCHEM_POLAR_SURFACE_AREA>
26.07

> <JCHEM_REFRACTIVITY>
34.0815

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,2-dimethyl-3,4-dihydropyrrol-1-ium-1-olate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

HMDB0246162
     RDKit          3D
5,5-Dimethyl-1-pyrroline N-oxide
 19 19  0  0  0  0  0  0  0  0999 V2000
   -1.3453   -1.2068   -0.6261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4090   -0.1592   -0.0493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1722    0.6426    0.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8435   -0.7696    0.4848 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8300    0.3878    0.3643 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3024    1.0701   -0.8458 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0762    0.7555   -1.0518 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.6772    1.2269   -2.0900 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.4028   -0.8859   -0.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2423   -2.0875    0.0739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0305   -1.5597   -1.6177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2226    0.7410    0.6192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7363    1.6674    1.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2092    0.1819    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1337   -1.6108   -0.1923 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7673   -1.1427    1.5213 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8523   -0.0089    0.2245 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7074    1.0158    1.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9347    1.7420   -1.4386 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  3 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
M  CHG  2   7   1   8  -1
M  END
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PDB for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

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       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+1
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O-1
HETATM    8  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6    8                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

COMPND    HMDB0246162
HETATM    1  C1  UNL     1      -1.345  -1.207  -0.626  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.409  -0.159  -0.049  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.172   0.643   0.972  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.843  -0.770   0.485  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.830   0.388   0.364  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.302   1.070  -0.846  1.00  0.00           C  
HETATM    7  N1  UNL     1       0.076   0.756  -1.052  1.00  0.00           N1+
HETATM    8  O1  UNL     1      -0.677   1.227  -2.090  1.00  0.00           O1-
HETATM    9  H1  UNL     1      -2.403  -0.886  -0.581  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.242  -2.087   0.074  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.031  -1.560  -1.618  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.223   0.741   0.619  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.736   1.667   1.009  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.209   0.182   1.965  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.134  -1.611  -0.192  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.767  -1.143   1.521  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.852  -0.009   0.225  1.00  0.00           H  
HETATM   18  H10 UNL     1       1.707   1.016   1.257  1.00  0.00           H  
HETATM   19  H11 UNL     1       1.935   1.742  -1.439  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4    7
CONECT    3   12   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7    7   19
CONECT    7    8
END
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SMILES for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

CC1(C)CCC=[N+]1[O-]
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INCHI for HMDB0246162 (5,5-Dimethyl-1-pyrroline N-oxide)

InChI=1S/C6H11NO/c1-6(2)4-3-5-7(6)8/h5H,3-4H2,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5,5-Dimethyl-1-pyrroline nitroneChEBI
5,5-Dimethyl-1-pyrroline-1-oxideChEBI
5,5-Dimethylpyrroline-N-oxideChEBI
DMPOChEBI
5,5-DMPOHMDB
5,5-Dimethyl-1-pyrroline-N-oxideHMDB
DMPO-5,5HMDB
Chemical FormulaC6H11NO
Average Molecular Weight113.16
Monoisotopic Molecular Weight113.084063978
IUPAC Name2,2-dimethyl-3,4-dihydro-2H-pyrrol-1-ium-1-olate
Traditional Name2,2-dimethyl-3,4-dihydropyrrol-1-ium-1-olate
CAS Registry NumberNot Available
SMILES
CC1(C)CCC=[N+]1[O-]
InChI Identifier
InChI=1S/C6H11NO/c1-6(2)4-3-5-7(6)8/h5H,3-4H2,1-2H3
InChI KeyVCUVETGKTILCLC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolines
Sub ClassNot Available
Direct ParentPyrrolines
Alternative Parents
Substituents
  • Pyrroline
  • Nitrone
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Allyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
logP0.34ALOGPS
logP-2.6ChemAxon
logS-0.96ALOGPS
pKa (Strongest Acidic)8.36ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity34.08 m³·mol⁻¹ChemAxon
Polarizability12.45 ųChemAxon
Number of Rings1ChemAxon
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]+132.3630932474
DeepCCS[M-H]-130.04130932474
DeepCCS[M-2H]-166.38630932474
DeepCCS[M+Na]+140.79330932474
AllCCS[M+H]+121.632859911
AllCCS[M+H-H2O]+116.832859911
AllCCS[M+NH4]+126.132859911
AllCCS[M+Na]+127.432859911
AllCCS[M-H]-123.632859911
AllCCS[M+Na-2H]-126.332859911
AllCCS[M+HCOO]-129.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5,5-Dimethyl-1-pyrroline N-oxideCC1(C)CCC=[N+]1[O-]1154.8Standard polar33892256
5,5-Dimethyl-1-pyrroline N-oxideCC1(C)CCC=[N+]1[O-]775.0Standard non polar33892256
5,5-Dimethyl-1-pyrroline N-oxideCC1(C)CCC=[N+]1[O-]914.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5,5-Dimethyl-1-pyrroline N-oxide GC-MS (Non-derivatized) - 70eV, Positivesplash10-002f-9000000000-90f59a08966a3e4353232021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,5-Dimethyl-1-pyrroline N-oxide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 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 NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 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 NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 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 NMR13C 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 NMR13C 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 NMR13C 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
Predicted 1D NMR13C 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 ID1709
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1774
PDB IDNot Available
ChEBI ID149489
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 ]