Hmdb loader

Showing metabocard for 1,3-Dinitroglycerin (HMDB0244171)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:21:13 UTC
Update Date2021-09-26 22:51:45 UTC
HMDB IDHMDB0244171
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,3-Dinitroglycerin
Description1,3-Glyceryl dinitrate, also known as 1,3-dinitroglycerin or 1,3-DNG, belongs to the class of organic compounds known as alkyl nitrates. These are organic compounds containing a nitrate that is O-linked to an alkyl group. Based on a literature review a significant number of articles have been published on 1,3-Glyceryl dinitrate. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,3-dinitroglycerin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,3-Dinitroglycerin 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 HMDB0244171 (1,3-Dinitroglycerin)


  Mrv1652310011601022D          

 12 11  0  0  0  0            999 V2000
    3.6829   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118   -0.0000    0.0000 N   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
    2.9684   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 10  5  2  0  0  0  0
 11  1  1  0  0  0  0
 11  4  1  0  0  0  0
 12  2  1  0  0  0  0
 12  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0244171 (1,3-Dinitroglycerin)

HMDB0244171
     RDKit          3D
1,3-Dinitroglycerin
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.9799   -0.9735    0.5844 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6197    0.1360    0.1770 N   0  0  0  0  0  4  0  0  0  0  0  0
    4.4692    1.2157    0.0924 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3220    0.3474   -0.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2129   -0.2985    0.3834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234    0.2121   -0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1175    1.5939   -0.2102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915   -0.4138    0.2007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3613    0.1142   -0.5713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6601   -0.1863   -0.4079 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.9924   -1.2870    0.0443 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6418    0.7016   -0.7314 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3537   -1.3838    0.2042 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -0.1275    1.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1095   -0.0065   -1.4266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5580    1.9612    0.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2733   -1.5097    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4370   -0.0954    1.2359 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  8 18  1  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
Download

3D SDF for HMDB0244171 (1,3-Dinitroglycerin)


  Mrv1652310011601022D          

 12 11  0  0  0  0            999 V2000
    3.6829   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118   -0.0000    0.0000 N   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
    2.9684   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  2  0  0  0  0
  9  5  2  0  0  0  0
 10  5  2  0  0  0  0
 11  1  1  0  0  0  0
 11  4  1  0  0  0  0
 12  2  1  0  0  0  0
 12  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244171

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(CON(=O)=O)CON(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H6N2O7/c6-3(1-11-4(7)8)2-12-5(9)10/h3,6H,1-2H2

> <INCHI_KEY>
ASIGVDLTBLZXNC-UHFFFAOYSA-N

> <FORMULA>
C3H6N2O7

> <MOLECULAR_WEIGHT>
182.088

> <EXACT_MASS>
182.017500541

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.353361225698588

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-(nitrooxy)propyl nitrate

> <ALOGPS_LOGP>
0.66

> <JCHEM_LOGP>
0.010889087333333339

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.476393953294398

> <JCHEM_PKA_STRONGEST_BASIC>
-3.46522528482903

> <JCHEM_POLAR_SURFACE_AREA>
130.33

> <JCHEM_REFRACTIVITY>
33.9041

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-(nitrooxy)propyl nitrate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0244171 (1,3-Dinitroglycerin)

HMDB0244171
     RDKit          3D
1,3-Dinitroglycerin
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.9799   -0.9735    0.5844 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6197    0.1360    0.1770 N   0  0  0  0  0  4  0  0  0  0  0  0
    4.4692    1.2157    0.0924 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3220    0.3474   -0.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2129   -0.2985    0.3834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234    0.2121   -0.3474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1175    1.5939   -0.2102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2915   -0.4138    0.2007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3613    0.1142   -0.5713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6601   -0.1863   -0.4079 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.9924   -1.2870    0.0443 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6418    0.7016   -0.7314 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3537   -1.3838    0.2042 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -0.1275    1.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1095   -0.0065   -1.4266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5580    1.9612    0.4127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2733   -1.5097    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4370   -0.0954    1.2359 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  8 17  1  0
  8 18  1  0
M  CHG  4   2   1   3  -1  10   1  12  -1
M  END
Download

PDB for HMDB0244171 (1,3-Dinitroglycerin)

HEADER    PROTEIN                                 01-OCT-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-OCT-16         0                                  
HETATM    1  C   UNK     0       6.875  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.207  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.541  -0.770   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       9.542  -0.000   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0       5.541  -2.310   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      10.876  -0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       9.542   1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.206  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       8.208  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.874  -0.770   0.000  0.00  0.00           O+0
CONECT    1    3   11                                                       
CONECT    2    3   12                                                       
CONECT    3    1    2    6                                                  
CONECT    4    7    8   11                                                  
CONECT    5    9   10   12                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    5                                                            
CONECT   11    1    4                                                       
CONECT   12    2    5                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
Download

3D PDB for HMDB0244171 (1,3-Dinitroglycerin)

COMPND    HMDB0244171
HETATM    1  O1  UNL     1       3.980  -0.974   0.584  1.00  0.00           O  
HETATM    2  N1  UNL     1       3.620   0.136   0.177  1.00  0.00           N1+
HETATM    3  O2  UNL     1       4.469   1.216   0.092  1.00  0.00           O1-
HETATM    4  O3  UNL     1       2.322   0.347  -0.220  1.00  0.00           O  
HETATM    5  C1  UNL     1       1.213  -0.299   0.383  1.00  0.00           C  
HETATM    6  C2  UNL     1      -0.023   0.212  -0.347  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.117   1.594  -0.210  1.00  0.00           O  
HETATM    8  C3  UNL     1      -1.291  -0.414   0.201  1.00  0.00           C  
HETATM    9  O5  UNL     1      -2.361   0.114  -0.571  1.00  0.00           O  
HETATM   10  N2  UNL     1      -3.660  -0.186  -0.408  1.00  0.00           N1+
HETATM   11  O6  UNL     1      -3.992  -1.287   0.044  1.00  0.00           O  
HETATM   12  O7  UNL     1      -4.642   0.702  -0.731  1.00  0.00           O1-
HETATM   13  H1  UNL     1       1.354  -1.384   0.204  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.173  -0.127   1.457  1.00  0.00           H  
HETATM   15  H3  UNL     1       0.110  -0.006  -1.427  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.558   1.961   0.413  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.273  -1.510   0.158  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.437  -0.095   1.236  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5
CONECT    5    6   13   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   17   18
CONECT    9   10
CONECT   10   11   11   12
END
Download

SMILES for HMDB0244171 (1,3-Dinitroglycerin)

OC(CON(=O)=O)CON(=O)=O
Download

INCHI for HMDB0244171 (1,3-Dinitroglycerin)

InChI=1S/C3H6N2O7/c6-3(1-11-4(7)8)2-12-5(9)10/h3,6H,1-2H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2,3-Propanetriol 1,3-dinitrateChEBI
1,2,3-Propanetriol, 1,3-dinitrateChEBI
1,3-DinitroglycerinChEBI
1,3-DNGChEBI
1,3-GDNChEBI
Glyceryl-1,3-dinitrateChEBI
1,2,3-Propanetriol 1,3-dinitric acidGenerator
1,2,3-Propanetriol, 1,3-dinitric acidGenerator
Glyceryl-1,3-dinitric acidGenerator
1,3-Glyceryl dinitric acidGenerator
1,3-Glyceryl dinitrateChEBI
Chemical FormulaC3H6N2O7
Average Molecular Weight182.088
Monoisotopic Molecular Weight182.017500541
IUPAC Name2-hydroxy-3-(nitrooxy)propyl nitrate
Traditional Name2-hydroxy-3-(nitrooxy)propyl nitrate
CAS Registry NumberNot Available
SMILES
OC(CON(=O)=O)CON(=O)=O
InChI Identifier
InChI=1S/C3H6N2O7/c6-3(1-11-4(7)8)2-12-5(9)10/h3,6H,1-2H2
InChI KeyASIGVDLTBLZXNC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkyl nitrates. These are organic compounds containing a nitrate that is O-linked to an alkyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic nitrates
Direct ParentAlkyl nitrates
Alternative Parents
Substituents
  • Alkyl nitrate
  • Organic nitro compound
  • Secondary alcohol
  • Organic nitric acid or derivatives
  • Organic 1,3-dipolar compound
  • Allyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic zwitterion
  • Organooxygen compound
  • Alcohol
  • 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
logP0.66ALOGPS
logP0.011ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)13.48ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area130.33 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity33.9 m³·mol⁻¹ChemAxon
Polarizability13.35 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]+131.40130932474
DeepCCS[M-H]-127.56830932474
DeepCCS[M-2H]-164.88830932474
DeepCCS[M+Na]+140.41630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-DinitroglycerinOC(CON(=O)=O)CON(=O)=O2433.5Standard polar33892256
1,3-DinitroglycerinOC(CON(=O)=O)CON(=O)=O1312.7Standard non polar33892256
1,3-DinitroglycerinOC(CON(=O)=O)CON(=O)=O1257.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitroglycerin GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9700000000-61f31878a8f3f0e916c42021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitroglycerin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitroglycerin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Dinitroglycerin GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 10V, Positive-QTOFsplash10-001i-0900000000-0411af1f75f1af1cd7942019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 20V, Positive-QTOFsplash10-00yi-2900000000-c858206256a1d096dc8d2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 40V, Positive-QTOFsplash10-0k96-9300000000-9a2da5287cbf4ef2ee7f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 10V, Negative-QTOFsplash10-001i-0900000000-78936930c4a5d8d5a4be2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 20V, Negative-QTOFsplash10-001i-1900000000-56165922a2b1ec39052f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Dinitroglycerin 40V, Negative-QTOFsplash10-0udi-5900000000-e845aaff0625d69be16c2019-02-23Wishart 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 ID11700
KEGG Compound IDNot Available
BioCyc IDCPD-145
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID18921
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 ]