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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:42:38 UTC

Update Date

2021-09-26 22:52:22 UTC

HMDB ID

HMDB0244560

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Desmethylmisonidazole

Description

3-(2-nitro-1H-imidazol-1-yl)propane-1,2-diol belongs to the class of organic compounds known as nitroaromatic compounds. These are c-nitro compounds where the nitro group is C-substituted with an aromatic group. Based on a literature review very few articles have been published on 3-(2-nitro-1H-imidazol-1-yl)propane-1,2-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Desmethylmisonidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Desmethylmisonidazole 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309102123422D          

 13 13  0  0  0  0            999 V2000
    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  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 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2820    0.5872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8951    0.0352    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3259   -0.4747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
M  CHG  2   6   1   8  -1
M  END
> <DATABASE_ID>
HMDB0244560

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(O)CN1C=CN=C1[N+]([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H9N3O4/c10-4-5(11)3-8-2-1-7-6(8)9(12)13/h1-2,5,10-11H,3-4H2

> <INCHI_KEY>
NUGLIYXAARVRPQ-UHFFFAOYSA-N

> <FORMULA>
C6H9N3O4

> <MOLECULAR_WEIGHT>
187.155

> <EXACT_MASS>
187.059305782

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.474835631368467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(2-nitro-1H-imidazol-1-yl)propane-1,2-diol

> <ALOGPS_LOGP>
-1.07

> <JCHEM_LOGP>
-0.6177509009999999

> <ALOGPS_LOGS>
-1.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.624842515529693

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.890227812649393

> <JCHEM_PKA_STRONGEST_BASIC>
-1.942561548516617

> <JCHEM_POLAR_SURFACE_AREA>
101.42

> <JCHEM_REFRACTIVITY>
41.9581

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(2-nitroimidazol-1-yl)propane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+1
HETATM    7  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O-1
HETATM    9  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.795   0.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.260   1.096   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.404   0.066   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.475  -0.886   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    3   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Demethylmisonidazole	MeSH

Chemical Formula

C₆H₉N₃O₄

Average Molecular Weight

187.155

Monoisotopic Molecular Weight

187.059305782

IUPAC Name

3-(2-nitro-1H-imidazol-1-yl)propane-1,2-diol

Traditional Name

3-(2-nitroimidazol-1-yl)propane-1,2-diol

CAS Registry Number

Not Available

SMILES

OCC(O)CN1C=CN=C1[N+]([O-])=O

InChI Identifier

InChI=1S/C6H9N3O4/c10-4-5(11)3-8-2-1-7-6(8)9(12)13/h1-2,5,10-11H,3-4H2

InChI Key

NUGLIYXAARVRPQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nitroaromatic compounds. These are c-nitro compounds where the nitro group is C-substituted with an aromatic group.

Kingdom

Organic compounds

Super Class

Organic 1,3-dipolar compounds

Class

Allyl-type 1,3-dipolar organic compounds

Sub Class

Organic nitro compounds

Direct Parent

Nitroaromatic compounds

Alternative Parents

Substituents

Nitroaromatic compound
N-substituted imidazole
Azole
Imidazole
Heteroaromatic compound
1,2-diol
Secondary alcohol
Organic oxoazanium
Azacycle
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Organic zwitterion
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.1	ALOGPS
logP	-0.62	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	-1.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	101.42 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	41.96 m³·mol⁻¹	ChemAxon
Polarizability	16.47 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	138.68	30932474
DeepCCS	[M-H]-	134.97	30932474
DeepCCS	[M-2H]-	171.815	30932474
DeepCCS	[M+Na]+	147.494	30932474
AllCCS	[M+H]+	140.8	32859911
AllCCS	[M+H-H2O]+	136.8	32859911
AllCCS	[M+NH4]+	144.6	32859911
AllCCS	[M+Na]+	145.6	32859911
AllCCS	[M-H]-	136.4	32859911
AllCCS	[M+Na-2H]-	137.2	32859911
AllCCS	[M+HCOO]-	138.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Desmethylmisonidazole	OCC(O)CN1C=CN=C1[N+]([O-])=O	2740.8	Standard polar	33892256
Desmethylmisonidazole	OCC(O)CN1C=CN=C1[N+]([O-])=O	1687.3	Standard non polar	33892256
Desmethylmisonidazole	OCC(O)CN1C=CN=C1[N+]([O-])=O	1758.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-8900000000-2a18c01949793058b9fd	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Desmethylmisonidazole GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

24318

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Desmethylmisonidazole (HMDB0244560)

MOL for HMDB0244560 (Desmethylmisonidazole)

3D MOL for HMDB0244560 (Desmethylmisonidazole)

3D SDF for HMDB0244560 (Desmethylmisonidazole)

3D-SDF for HMDB0244560 (Desmethylmisonidazole)

PDB for HMDB0244560 (Desmethylmisonidazole)

3D PDB for HMDB0244560 (Desmethylmisonidazole)

SMILES for HMDB0244560 (Desmethylmisonidazole)

INCHI for HMDB0244560 (Desmethylmisonidazole)

Structure for HMDB0244560 (Desmethylmisonidazole)

3D Structure for HMDB0244560 (Desmethylmisonidazole)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

NMR Spectra