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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 17:04:13 UTC

Update Date

2022-09-22 17:44:26 UTC

HMDB ID

HMDB0256554

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Pimonidazole

Description

Pimonidazole 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 a significant number of articles have been published on Pimonidazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pimonidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pimonidazole 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

HMDB0256554
     RDKit          3D
Pimonidazole
 36 37  0  0  0  0  0  0  0  0999 V2000
   -5.6698    1.2900   -0.3851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4869    1.0410   -0.0012 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.7024    2.1312    0.2000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.0722   -0.3061    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8960   -1.3748   -0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2457   -2.5083    0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9776   -2.1243    0.6247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8959   -0.7675    0.5795 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7083   -0.0490    0.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7544    0.1118   -0.2915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4073    0.7858   -1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4639    0.7708    0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5052    1.0280   -0.6609 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6595    1.6681   -0.1263 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4706    0.6191    0.6105 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6934   -0.5493   -0.3218 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2200   -0.2144   -1.7370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497    0.1668   -1.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5697   -3.5388    0.1985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1915   -2.7934    0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9849    0.9640    1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960   -0.5711    1.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5213   -0.9499   -0.5986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5227    0.2489   -2.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1933    1.7237    0.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8576    0.1136    1.0659 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3178    2.1182   -0.9085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4004    2.5229    0.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4264    1.0715    0.9459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8511    0.2633    1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7726   -0.7331   -0.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1683   -1.4682    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8811    0.5767   -2.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4051   -1.1348   -2.3300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1751   -0.7871   -1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5914    0.6545   -2.7562 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  8  4  1  0
 18 13  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
 15 29  1  0
 15 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 18 35  1  0
 18 36  1  0
M  CHG  2   2   1   3  -1
M  END


  Mrv1533004261507012D          

 18 19  0  0  0  0            999 V2000
    1.5356    8.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5356    7.2402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212    6.8277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1067    7.2402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1067    8.0652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212    8.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    6.8277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    6.0027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    4.2803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    3.4956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    3.4956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    4.2803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    4.5352    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -3.3874    3.9832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9458    5.3422    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1067    5.5902    0.0000 O   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  1  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  8 18  1  0  0  0  0
M  CHG  2  15   1  17  -1
M  END
> <DATABASE_ID>
HMDB0256554

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(CN1C=CN=C1[N+]([O-])=O)CN1CCCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N4O3/c16-10(8-13-5-2-1-3-6-13)9-14-7-4-12-11(14)15(17)18/h4,7,10,16H,1-3,5-6,8-9H2

> <INCHI_KEY>
WVWOOAYQYLJEFD-UHFFFAOYSA-N

> <FORMULA>
C11H18N4O3

> <MOLECULAR_WEIGHT>
254.29

> <EXACT_MASS>
254.137890456

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
25.315420872049348

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2-nitro-1H-imidazol-1-yl)-3-(piperidin-1-yl)propan-2-ol

> <ALOGPS_LOGP>
0.58

> <JCHEM_LOGP>
0.9413617650000006

> <ALOGPS_LOGS>
-1.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.385208013427256

> <JCHEM_PKA_STRONGEST_BASIC>
8.762944567125505

> <JCHEM_POLAR_SURFACE_AREA>
84.43

> <JCHEM_REFRACTIVITY>
65.82690000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.92e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pimonidazole

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256554
     RDKit          3D
Pimonidazole
 36 37  0  0  0  0  0  0  0  0999 V2000
   -5.6698    1.2900   -0.3851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4869    1.0410   -0.0012 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.7024    2.1312    0.2000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.0722   -0.3061    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8960   -1.3748   -0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2457   -2.5083    0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9776   -2.1243    0.6247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8959   -0.7675    0.5795 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7083   -0.0490    0.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7544    0.1118   -0.2915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4073    0.7858   -1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4639    0.7708    0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5052    1.0280   -0.6609 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6595    1.6681   -0.1263 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4706    0.6191    0.6105 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6934   -0.5493   -0.3218 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2200   -0.2144   -1.7370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497    0.1668   -1.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5697   -3.5388    0.1985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1915   -2.7934    0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9849    0.9640    1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960   -0.5711    1.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5213   -0.9499   -0.5986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5227    0.2489   -2.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1933    1.7237    0.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8576    0.1136    1.0659 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3178    2.1182   -0.9085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4004    2.5229    0.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4264    1.0715    0.9459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8511    0.2633    1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7726   -0.7331   -0.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1683   -1.4682    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8811    0.5767   -2.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4051   -1.1348   -2.3300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1751   -0.7871   -1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5914    0.6545   -2.7562 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  8  4  1  0
 18 13  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
 15 29  1  0
 15 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 18 35  1  0
 18 36  1  0
M  CHG  2   2   1   3  -1
M  END

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       2.867  15.055   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.867  13.515   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.533  12.745   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.199  13.515   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.199  15.055   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.533  15.825   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.134  12.745   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.134  11.205   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.468  10.435   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -2.468   8.895   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.222   7.990   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.698   6.525   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -3.238   6.525   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -3.714   7.990   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -5.179   8.466   0.000  0.00  0.00           N+1
HETATM   16  O   UNK     0      -6.323   7.435   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -5.499   9.972   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       0.199  10.435   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10   15                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18    8                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0256554
HETATM    1  O1  UNL     1      -5.670   1.290  -0.385  1.00  0.00           O  
HETATM    2  N1  UNL     1      -4.487   1.041  -0.001  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -3.702   2.131   0.200  1.00  0.00           O1-
HETATM    4  C1  UNL     1      -4.072  -0.306   0.187  1.00  0.00           C  
HETATM    5  N2  UNL     1      -4.896  -1.375  -0.016  1.00  0.00           N  
HETATM    6  C2  UNL     1      -4.246  -2.508   0.247  1.00  0.00           C  
HETATM    7  C3  UNL     1      -2.978  -2.124   0.625  1.00  0.00           C  
HETATM    8  N3  UNL     1      -2.896  -0.768   0.579  1.00  0.00           N  
HETATM    9  C4  UNL     1      -1.708  -0.049   0.891  1.00  0.00           C  
HETATM   10  C5  UNL     1      -0.754   0.112  -0.292  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.407   0.786  -1.283  1.00  0.00           O  
HETATM   12  C6  UNL     1       0.464   0.771   0.234  1.00  0.00           C  
HETATM   13  N4  UNL     1       1.505   1.028  -0.661  1.00  0.00           N  
HETATM   14  C7  UNL     1       2.659   1.668  -0.126  1.00  0.00           C  
HETATM   15  C8  UNL     1       3.471   0.619   0.610  1.00  0.00           C  
HETATM   16  C9  UNL     1       3.693  -0.549  -0.322  1.00  0.00           C  
HETATM   17  C10 UNL     1       3.220  -0.214  -1.737  1.00  0.00           C  
HETATM   18  C11 UNL     1       1.750   0.167  -1.749  1.00  0.00           C  
HETATM   19  H1  UNL     1      -4.570  -3.539   0.198  1.00  0.00           H  
HETATM   20  H2  UNL     1      -2.192  -2.793   0.907  1.00  0.00           H  
HETATM   21  H3  UNL     1      -1.985   0.964   1.301  1.00  0.00           H  
HETATM   22  H4  UNL     1      -1.196  -0.571   1.737  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.521  -0.950  -0.599  1.00  0.00           H  
HETATM   24  H6  UNL     1      -1.523   0.249  -2.122  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.193   1.724   0.764  1.00  0.00           H  
HETATM   26  H8  UNL     1       0.858   0.114   1.066  1.00  0.00           H  
HETATM   27  H9  UNL     1       3.318   2.118  -0.909  1.00  0.00           H  
HETATM   28  H10 UNL     1       2.400   2.523   0.552  1.00  0.00           H  
HETATM   29  H11 UNL     1       4.426   1.071   0.946  1.00  0.00           H  
HETATM   30  H12 UNL     1       2.851   0.263   1.454  1.00  0.00           H  
HETATM   31  H13 UNL     1       4.773  -0.733  -0.389  1.00  0.00           H  
HETATM   32  H14 UNL     1       3.168  -1.468   0.030  1.00  0.00           H  
HETATM   33  H15 UNL     1       3.881   0.577  -2.111  1.00  0.00           H  
HETATM   34  H16 UNL     1       3.405  -1.135  -2.330  1.00  0.00           H  
HETATM   35  H17 UNL     1       1.175  -0.787  -1.690  1.00  0.00           H  
HETATM   36  H18 UNL     1       1.591   0.655  -2.756  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    8
CONECT    5    6
CONECT    6    7    7   19
CONECT    7    8   20
CONECT    8    9
CONECT    9   10   21   22
CONECT   10   11   12   23
CONECT   11   24
CONECT   12   13   25   26
CONECT   13   14   18
CONECT   14   15   27   28
CONECT   15   16   29   30
CONECT   16   17   31   32
CONECT   17   18   33   34
CONECT   18   35   36
END

HMDB0256554
     RDKit          3D
Pimonidazole
 36 37  0  0  0  0  0  0  0  0999 V2000
   -5.6698    1.2900   -0.3851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4869    1.0410   -0.0012 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.7024    2.1312    0.2000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.0722   -0.3061    0.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8960   -1.3748   -0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2457   -2.5083    0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9776   -2.1243    0.6247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8959   -0.7675    0.5795 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7083   -0.0490    0.8906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7544    0.1118   -0.2915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4073    0.7858   -1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4639    0.7708    0.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5052    1.0280   -0.6609 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6595    1.6681   -0.1263 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4706    0.6191    0.6105 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6934   -0.5493   -0.3218 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2200   -0.2144   -1.7370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497    0.1668   -1.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5697   -3.5388    0.1985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1915   -2.7934    0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9849    0.9640    1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960   -0.5711    1.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5213   -0.9499   -0.5986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5227    0.2489   -2.1216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1933    1.7237    0.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8576    0.1136    1.0659 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3178    2.1182   -0.9085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4004    2.5229    0.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4264    1.0715    0.9459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8511    0.2633    1.4544 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7726   -0.7331   -0.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1683   -1.4682    0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8811    0.5767   -2.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4051   -1.1348   -2.3300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1751   -0.7871   -1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5914    0.6545   -2.7562 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  8  4  1  0
 18 13  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 14 27  1  0
 14 28  1  0
 15 29  1  0
 15 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 18 35  1  0
 18 36  1  0
M  CHG  2   2   1   3  -1
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
ro-038799SID470365	ChEMBL
2-((Nitroimidazol-1-yl)methyl)-1-piperdineethanol	MeSH
2-Nitro-alpha-(piperidinomethyl)-1-imidazole ethanol	MeSH
2-Pimonidazole	MeSH
Hypoxyprobe-1	MeSH

Chemical Formula

C₁₁H₁₈N₄O₃

Average Molecular Weight

254.29

Monoisotopic Molecular Weight

254.137890456

IUPAC Name

1-(2-nitro-1H-imidazol-1-yl)-3-(piperidin-1-yl)propan-2-ol

Traditional Name

pimonidazole

CAS Registry Number

Not Available

SMILES

OC(CN1C=CN=C1[N+]([O-])=O)CN1CCCCC1

InChI Identifier

InChI=1S/C11H18N4O3/c16-10(8-13-5-2-1-3-6-13)9-14-7-4-12-11(14)15(17)18/h4,7,10,16H,1-3,5-6,8-9H2

InChI Key

WVWOOAYQYLJEFD-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
Piperidine
Azole
Imidazole
Heteroaromatic compound
1,2-aminoalcohol
Secondary alcohol
Tertiary amine
Tertiary aliphatic amine
Organic oxoazanium
Propargyl-type 1,3-dipolar organic compound
Organoheterocyclic compound
Azacycle
Organic zwitterion
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Organopnictogen compound
Amine
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)

Source

Exogenous

Exogenous (HMDB: HMDB0256554)

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	0.58	ALOGPS
logP	0.94	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	14.39	ChemAxon
pKa (Strongest Basic)	8.76	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	84.43 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	65.83 m³·mol⁻¹	ChemAxon
Polarizability	25.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	153.851	30932474
DeepCCS	[M-H]-	151.456	30932474
DeepCCS	[M-2H]-	184.596	30932474
DeepCCS	[M+Na]+	159.764	30932474
AllCCS	[M+H]+	157.9	32859911
AllCCS	[M+H-H2O]+	154.3	32859911
AllCCS	[M+NH4]+	161.3	32859911
AllCCS	[M+Na]+	162.3	32859911
AllCCS	[M-H]-	159.4	32859911
AllCCS	[M+Na-2H]-	159.5	32859911
AllCCS	[M+HCOO]-	159.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	2.1 minutes	32390414
Predicted by Siyang on May 30, 2022	9.2811 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	4.4 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	528.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	221.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	105.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	159.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	51.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	250.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	292.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	441.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	628.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	43.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	821.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	164.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	198.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	737.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	472.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	232.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pimonidazole	OC(CN1C=CN=C1[N+]([O-])=O)CN1CCCCC1	2455.7	Standard polar	33892256
Pimonidazole	OC(CN1C=CN=C1[N+]([O-])=O)CN1CCCCC1	2050.5	Standard non polar	33892256
Pimonidazole	OC(CN1C=CN=C1[N+]([O-])=O)CN1CCCCC1	2137.7	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 - Pimonidazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-0005-9310000000-c177e336f3ed2a330e69	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pimonidazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pimonidazole GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pimonidazole GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 10V, Positive-QTOF	splash10-0a4i-0090000000-968d1887b6d7d4d89417	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 20V, Positive-QTOF	splash10-002f-1290000000-4e30e3fe8f2954e7ef26	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 40V, Positive-QTOF	splash10-002o-9320000000-aaa06b8bea1c9bbc78c0	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 10V, Negative-QTOF	splash10-0udi-1090000000-bbde1e4c00a97b243c38	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 20V, Negative-QTOF	splash10-0ff3-4190000000-1a66cdb2a1e08a266682	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pimonidazole 40V, Negative-QTOF	splash10-001i-9000000000-71015c630c0ae8500b00	2017-07-26	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-27	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

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

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB12485

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

46214

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 Pimonidazole (HMDB0256554)

MOL for HMDB0256554 (Pimonidazole)

3D MOL for HMDB0256554 (Pimonidazole)

3D SDF for HMDB0256554 (Pimonidazole)

3D-SDF for HMDB0256554 (Pimonidazole)

PDB for HMDB0256554 (Pimonidazole)

3D PDB for HMDB0256554 (Pimonidazole)

SMILES for HMDB0256554 (Pimonidazole)

INCHI for HMDB0256554 (Pimonidazole)

Structure for HMDB0256554 (Pimonidazole)

3D Structure for HMDB0256554 (Pimonidazole)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra