Hmdb loader

Showing metabocard for Secnidazole (HMDB0258202)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 19:26:27 UTC
Update Date2021-09-26 23:14:57 UTC
HMDB IDHMDB0258202
Secondary Accession NumbersNone
Metabolite Identification
Common NameSecnidazole
DescriptionSecnidazole, also known as secnidal or solosec, belongs to the class of organic compounds known as nitroimidazoles. Nitroimidazoles are compounds containing an imidazole ring which bears a nitro group. Based on a literature review a significant number of articles have been published on Secnidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). Secnidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Secnidazole 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 HMDB0258202 (Secnidazole)

  Mrv1572004221605012D          

 13 13  0  0  0  0            999 V2000
   -2.2820    0.5872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    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
   -0.8843    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
    0.1553   -0.1553    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
    0.9803   -0.1553    0.0000 N   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    1.9393    0.0000 N   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
   -0.1467    2.3518    0.0000 O   0  0  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
  5  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
  8  6  2  0  0  0  0
  9  4  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  7  1  0  0  0  0
 11  5  1  0  0  0  0
 12 10  2  0  0  0  0
 13 10  2  0  0  0  0
M  END
Download

3D MOL for HMDB0258202 (Secnidazole)

HMDB0258202
     RDKit          3D
Secnidazole
 24 24  0  0  0  0  0  0  0  0999 V2000
    0.9586    2.4257   -0.5701 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4854    1.0157   -0.4359 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6702    0.6199   -0.8909 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8296   -0.6725   -0.6125 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6835   -1.0824    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4735   -2.3978    0.5040 N   0  0  0  0  0  4  0  0  0  0  0  0
    0.4222   -2.6881    1.0811 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4191   -3.3550    0.3167 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.8535   -0.0082    0.1452 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4336    0.0509    0.7448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5850   -0.2584   -0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8567   -0.1349    0.6981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7443    0.5869   -1.2263 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2503    2.4561   -1.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8187    3.1117   -0.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4505    2.6841    0.3807 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6960   -1.3128   -0.8490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5962    1.1089    1.1060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5057   -0.6308    1.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5830   -1.2954   -0.5384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7419    0.6388    1.4793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0773   -1.0876    1.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7319    0.0836    0.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1556    0.1416   -2.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
  9  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  0
 10 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 12 22  1  0
 12 23  1  0
 13 24  1  0
M  CHG  2   6   1   8  -1
M  END
Download

3D SDF for HMDB0258202 (Secnidazole)

  Mrv1572004221605012D          

 13 13  0  0  0  0            999 V2000
   -2.2820    0.5872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    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
   -0.8843    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
    0.1553   -0.1553    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
    0.9803   -0.1553    0.0000 N   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    1.9393    0.0000 N   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
   -0.1467    2.3518    0.0000 O   0  0  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
  5  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
  8  6  2  0  0  0  0
  9  4  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  7  1  0  0  0  0
 11  5  1  0  0  0  0
 12 10  2  0  0  0  0
 13 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258202

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)CN1C(C)=NC=C1N(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H11N3O3/c1-5(11)4-9-6(2)8-3-7(9)10(12)13/h3,5,11H,4H2,1-2H3

> <INCHI_KEY>
KPQZUUQMTUIKBP-UHFFFAOYSA-N

> <FORMULA>
C7H11N3O3

> <MOLECULAR_WEIGHT>
185.183

> <EXACT_MASS>
185.080041226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.56874438181771

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2-methyl-5-nitro-1H-imidazol-1-yl)propan-2-ol

> <ALOGPS_LOGP>
0.25

> <JCHEM_LOGP>
-0.04273520000000014

> <ALOGPS_LOGS>
-1.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.158427567329909

> <JCHEM_PKA_STRONGEST_BASIC>
3.0849497376110038

> <JCHEM_POLAR_SURFACE_AREA>
83.87

> <JCHEM_REFRACTIVITY>
45.6393

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.88e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
secnidazole

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0258202 (Secnidazole)

HMDB0258202
     RDKit          3D
Secnidazole
 24 24  0  0  0  0  0  0  0  0999 V2000
    0.9586    2.4257   -0.5701 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4854    1.0157   -0.4359 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6702    0.6199   -0.8909 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8296   -0.6725   -0.6125 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6835   -1.0824    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4735   -2.3978    0.5040 N   0  0  0  0  0  4  0  0  0  0  0  0
    0.4222   -2.6881    1.0811 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4191   -3.3550    0.3167 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.8535   -0.0082    0.1452 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4336    0.0509    0.7448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5850   -0.2584   -0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8567   -0.1349    0.6981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7443    0.5869   -1.2263 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2503    2.4561   -1.4133 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8187    3.1117   -0.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4505    2.6841    0.3807 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6960   -1.3128   -0.8490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5962    1.1089    1.1060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5057   -0.6308    1.6190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5830   -1.2954   -0.5384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7419    0.6388    1.4793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0773   -1.0876    1.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7319    0.0836    0.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1556    0.1416   -2.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
  9  2  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  4 17  1  0
 10 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 12 22  1  0
 12 23  1  0
 13 24  1  0
M  CHG  2   6   1   8  -1
M  END
Download

PDB for HMDB0258202 (Secnidazole)

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0      -4.260   1.096   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.615  -1.536   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      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.795   0.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      -2.475  -0.886   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    7    8                                                       
CONECT    4    5    9                                                       
CONECT    5    1    4   11                                                  
CONECT    6    2    8    9                                                  
CONECT    7    3    9   10                                                  
CONECT    8    3    6                                                       
CONECT    9    4    6    7                                                  
CONECT   10    7   12   13                                                  
CONECT   11    5                                                            
CONECT   12   10                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
Download

3D PDB for HMDB0258202 (Secnidazole)

COMPND    HMDB0258202
HETATM    1  C1  UNL     1       0.959   2.426  -0.570  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.485   1.016  -0.436  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.670   0.620  -0.891  1.00  0.00           N  
HETATM    4  C3  UNL     1       2.830  -0.673  -0.612  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.684  -1.082   0.045  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.474  -2.398   0.504  1.00  0.00           N1+
HETATM    7  O1  UNL     1       0.422  -2.688   1.081  1.00  0.00           O  
HETATM    8  O2  UNL     1       2.419  -3.355   0.317  1.00  0.00           O1-
HETATM    9  N3  UNL     1       0.854  -0.008   0.145  1.00  0.00           N  
HETATM   10  C5  UNL     1      -0.434   0.051   0.745  1.00  0.00           C  
HETATM   11  C6  UNL     1      -1.585  -0.258  -0.153  1.00  0.00           C  
HETATM   12  C7  UNL     1      -2.857  -0.135   0.698  1.00  0.00           C  
HETATM   13  O3  UNL     1      -1.744   0.587  -1.226  1.00  0.00           O  
HETATM   14  H1  UNL     1       0.250   2.456  -1.413  1.00  0.00           H  
HETATM   15  H2  UNL     1       1.819   3.112  -0.705  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.451   2.684   0.381  1.00  0.00           H  
HETATM   17  H4  UNL     1       3.696  -1.313  -0.849  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.596   1.109   1.106  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.506  -0.631   1.619  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.583  -1.295  -0.538  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.742   0.639   1.479  1.00  0.00           H  
HETATM   22  H9  UNL     1      -3.077  -1.088   1.222  1.00  0.00           H  
HETATM   23  H10 UNL     1      -3.732   0.084   0.058  1.00  0.00           H  
HETATM   24  H11 UNL     1      -2.156   0.142  -2.007  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3    3    9
CONECT    3    4
CONECT    4    5    5   17
CONECT    5    6    9
CONECT    6    7    7    8
CONECT    9   10
CONECT   10   11   18   19
CONECT   11   12   13   20
CONECT   12   21   22   23
CONECT   13   24
END
Download

SMILES for HMDB0258202 (Secnidazole)

CC(O)CN1C(C)=NC=C1N(=O)=O
Download

INCHI for HMDB0258202 (Secnidazole)

InChI=1S/C7H11N3O3/c1-5(11)4-9-6(2)8-3-7(9)10(12)13/h3,5,11H,4H2,1-2H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
SecnidazolChEBI
SecnidazolumChEBI
SecnidalKegg
SolosecKegg
SecnolMeSH
MinovagMeSH
1-(2'-Hydroxypropyl)-2-methyl-5- nitroimidazoleMeSH
SecnidazoleMeSH
SabimaMeSH
Chemical FormulaC7H11N3O3
Average Molecular Weight185.183
Monoisotopic Molecular Weight185.080041226
IUPAC Name1-(2-methyl-5-nitro-1H-imidazol-1-yl)propan-2-ol
Traditional Namesecnidazole
CAS Registry NumberNot Available
SMILES
CC(O)CN1C(C)=NC=C1N(=O)=O
InChI Identifier
InChI=1S/C7H11N3O3/c1-5(11)4-9-6(2)8-3-7(9)10(12)13/h3,5,11H,4H2,1-2H3
InChI KeyKPQZUUQMTUIKBP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitroimidazoles. Nitroimidazoles are compounds containing an imidazole ring which bears a nitro group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentNitroimidazoles
Alternative Parents
Substituents
  • 1,2,5-trisubstituted-imidazole
  • Nitroaromatic compound
  • Nitroimidazole
  • Trisubstituted imidazole
  • N-substituted imidazole
  • Heteroaromatic compound
  • C-nitro compound
  • Secondary alcohol
  • Organic nitro compound
  • Organic oxoazanium
  • Azacycle
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organic oxide
  • Alcohol
  • Organic zwitterion
  • Organic oxygen compound
  • Organopnictogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
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 IDDB12834
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID64839
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSecnidazole
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID140628
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 ]