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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 15:29:50 UTC

Update Date

2021-09-26 23:10:44 UTC

HMDB ID

HMDB0255688

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Nocodazole

Description

Nocodazole, also known as R 17934, belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). Based on a literature review a significant number of articles have been published on Nocodazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). Nocodazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Nocodazole 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

HMDB0255688
     RDKit          3D
Nocodazole
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.9560    1.4735    0.6327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539    0.6230    0.3854 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0778   -0.6544   -0.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2792   -1.0596   -0.2608 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0434   -1.5749   -0.3449 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6694   -1.2439   -0.1762 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6451   -2.1052   -0.4358 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4737   -1.4993   -0.1855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8403   -1.8866   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8592   -1.0067    0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6102    0.2774    0.4870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7462    1.1310    0.7986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6871    2.0861    1.6072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0376    0.8839    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2143    0.4234    0.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2631    0.3249   -0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0789    0.6937   -1.4633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4365    1.1661   -1.4943 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2908    0.6696    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7344   -0.2178    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0819   -0.1107    0.2352 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6770    2.5376    0.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8440    1.2292    0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1922    1.4555    1.7267 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2954   -2.5234   -0.6836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0404   -2.8936   -0.6185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8690   -1.3927   -0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2623    0.1437    1.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2644   -0.0402    0.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8285    0.6823   -2.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0742    1.6596    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5796    0.7484    0.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 11 19  1  0
 19 20  2  0
 20 21  1  0
 21  6  1  0
 20  8  1  0
 18 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
 19 31  1  0
 21 32  1  0
M  END

NZO
  Mrv0541 02241214002D          

 21 23  0  0  0  0            999 V2000
   -1.9576   -1.9285    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3701   -1.2140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1951   -1.2140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6076   -1.9285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9576   -0.4996    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1326   -0.4996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6477    0.1679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1370   -0.0871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514    0.3254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6477   -1.1670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1370   -0.9121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514   -1.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5659   -0.9121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5659   -0.0871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2804    0.3254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9948   -0.0871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2804    1.1504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9478    1.6354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6929    2.4200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8679    2.4200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6129    1.6354    0.0000 S   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
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 14  1  0  0  0  0
 10  6  2  0  0  0  0
 10 11  1  0  0  0  0
 11  8  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
 14 15  1  0  0  0  0
 15 17  1  0  0  0  0
 15 16  2  0  0  0  0
 17 21  1  0  0  0  0
 18 17  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255688

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)NC1=NC2=CC=C(C=C2N1)C(=O)C1=CC=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C14H11N3O3S/c1-20-14(19)17-13-15-9-5-4-8(7-10(9)16-13)12(18)11-3-2-6-21-11/h2-7H,1H3,(H2,15,16,17,19)

> <INCHI_KEY>
KYRVNWMVYQXFEU-UHFFFAOYSA-N

> <FORMULA>
C14H11N3O3S

> <MOLECULAR_WEIGHT>
301.32

> <EXACT_MASS>
301.052111923

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
30.92973411142622

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl N-[6-(thiophene-2-carbonyl)-1H-1,3-benzodiazol-2-yl]carbamate

> <ALOGPS_LOGP>
2.84

> <JCHEM_LOGP>
3.1729899176666665

> <ALOGPS_LOGS>
-4.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.922287380085297

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.340342016999017

> <JCHEM_PKA_STRONGEST_BASIC>
3.900582455845347

> <JCHEM_POLAR_SURFACE_AREA>
84.07999999999998

> <JCHEM_REFRACTIVITY>
78.39380000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.85e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nocodazole

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0255688
     RDKit          3D
Nocodazole
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.9560    1.4735    0.6327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539    0.6230    0.3854 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0778   -0.6544   -0.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2792   -1.0596   -0.2608 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0434   -1.5749   -0.3449 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6694   -1.2439   -0.1762 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6451   -2.1052   -0.4358 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4737   -1.4993   -0.1855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8403   -1.8866   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8592   -1.0067    0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6102    0.2774    0.4870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7462    1.1310    0.7986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6871    2.0861    1.6072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0376    0.8839    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2143    0.4234    0.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2631    0.3249   -0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0789    0.6937   -1.4633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4365    1.1661   -1.4943 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2908    0.6696    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7344   -0.2178    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0819   -0.1107    0.2352 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6770    2.5376    0.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8440    1.2292    0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1922    1.4555    1.7267 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2954   -2.5234   -0.6836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0404   -2.8936   -0.6185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8690   -1.3927   -0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2623    0.1437    1.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2644   -0.0402    0.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8285    0.6823   -2.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0742    1.6596    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5796    0.7484    0.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 11 19  1  0
 19 20  2  0
 20 21  1  0
 21  6  1  0
 20  8  1  0
 18 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
 19 31  1  0
 21 32  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: NZO                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -3.654  -3.600   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.424  -2.266   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -5.964  -2.266   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -6.734  -3.600   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -3.654  -0.933   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.114  -0.933   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.209   0.313   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.256  -0.163   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.589   0.607   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -1.209  -2.178   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       0.256  -1.703   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.589  -2.473   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.923  -1.703   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.923  -0.163   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.257   0.607   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.590  -0.163   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.257   2.147   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.503   3.053   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.027   4.517   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.487   4.517   0.000  0.00  0.00           C+0
HETATM   21  S   UNK     0       3.011   3.053   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   14                                                       
CONECT   10    6   11                                                       
CONECT   11   10    8   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14    9   13   15                                                  
CONECT   15   14   17   16                                                  
CONECT   16   15                                                            
CONECT   17   15   21   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   17   20                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

COMPND    HMDB0255688
HETATM    1  C1  UNL     1       5.956   1.474   0.633  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.854   0.623   0.385  1.00  0.00           O  
HETATM    3  C2  UNL     1       5.078  -0.654  -0.068  1.00  0.00           C  
HETATM    4  O2  UNL     1       6.279  -1.060  -0.261  1.00  0.00           O  
HETATM    5  N1  UNL     1       4.043  -1.575  -0.345  1.00  0.00           N  
HETATM    6  C3  UNL     1       2.669  -1.244  -0.176  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.645  -2.105  -0.436  1.00  0.00           N  
HETATM    8  C4  UNL     1       0.474  -1.499  -0.186  1.00  0.00           C  
HETATM    9  C5  UNL     1      -0.840  -1.887  -0.280  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.859  -1.007   0.053  1.00  0.00           C  
HETATM   11  C7  UNL     1      -1.610   0.277   0.487  1.00  0.00           C  
HETATM   12  C8  UNL     1      -2.746   1.131   0.799  1.00  0.00           C  
HETATM   13  O3  UNL     1      -2.687   2.086   1.607  1.00  0.00           O  
HETATM   14  C9  UNL     1      -4.038   0.884   0.146  1.00  0.00           C  
HETATM   15  C10 UNL     1      -5.214   0.423   0.668  1.00  0.00           C  
HETATM   16  C11 UNL     1      -6.263   0.325  -0.155  1.00  0.00           C  
HETATM   17  C12 UNL     1      -6.079   0.694  -1.463  1.00  0.00           C  
HETATM   18  S1  UNL     1      -4.436   1.166  -1.494  1.00  0.00           S  
HETATM   19  C13 UNL     1      -0.291   0.670   0.582  1.00  0.00           C  
HETATM   20  C14 UNL     1       0.734  -0.218   0.246  1.00  0.00           C  
HETATM   21  N3  UNL     1       2.082  -0.111   0.235  1.00  0.00           N  
HETATM   22  H1  UNL     1       5.677   2.538   0.398  1.00  0.00           H  
HETATM   23  H2  UNL     1       6.844   1.229   0.028  1.00  0.00           H  
HETATM   24  H3  UNL     1       6.192   1.455   1.727  1.00  0.00           H  
HETATM   25  H4  UNL     1       4.295  -2.523  -0.684  1.00  0.00           H  
HETATM   26  H5  UNL     1      -1.040  -2.894  -0.618  1.00  0.00           H  
HETATM   27  H6  UNL     1      -2.869  -1.393  -0.045  1.00  0.00           H  
HETATM   28  H7  UNL     1      -5.262   0.144   1.749  1.00  0.00           H  
HETATM   29  H8  UNL     1      -7.264  -0.040   0.162  1.00  0.00           H  
HETATM   30  H9  UNL     1      -6.829   0.682  -2.277  1.00  0.00           H  
HETATM   31  H10 UNL     1      -0.074   1.660   0.917  1.00  0.00           H  
HETATM   32  H11 UNL     1       2.580   0.748   0.514  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6   25
CONECT    6    7    7   21
CONECT    7    8
CONECT    8    9    9   20
CONECT    9   10   26
CONECT   10   11   11   27
CONECT   11   12   19
CONECT   12   13   13   14
CONECT   14   15   15   18
CONECT   15   16   28
CONECT   16   17   17   29
CONECT   17   18   30
CONECT   19   20   20   31
CONECT   20   21
CONECT   21   32
END

HMDB0255688
     RDKit          3D
Nocodazole
 32 34  0  0  0  0  0  0  0  0999 V2000
    5.9560    1.4735    0.6327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539    0.6230    0.3854 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0778   -0.6544   -0.0682 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2792   -1.0596   -0.2608 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0434   -1.5749   -0.3449 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6694   -1.2439   -0.1762 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6451   -2.1052   -0.4358 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4737   -1.4993   -0.1855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8403   -1.8866   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8592   -1.0067    0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6102    0.2774    0.4870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7462    1.1310    0.7986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6871    2.0861    1.6072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0376    0.8839    0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2143    0.4234    0.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2631    0.3249   -0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0789    0.6937   -1.4633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4365    1.1661   -1.4943 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2908    0.6696    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7344   -0.2178    0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0819   -0.1107    0.2352 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6770    2.5376    0.3976 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8440    1.2292    0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1922    1.4555    1.7267 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2954   -2.5234   -0.6836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0404   -2.8936   -0.6185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8690   -1.3927   -0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2623    0.1437    1.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2644   -0.0402    0.1624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8285    0.6823   -2.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0742    1.6596    0.9171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5796    0.7484    0.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 11 19  1  0
 19 20  2  0
 20 21  1  0
 21  6  1  0
 20  8  1  0
 18 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  5 25  1  0
  9 26  1  0
 10 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
 19 31  1  0
 21 32  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(5-(2-Thienylcarbonyl)-1H-benzimidazol-2-yl)-carbamic acid methyl ester	ChEBI
Methyl (5-(2-thienylcarbonyl))-1H-benzimidazole-2-ylcarbamate	ChEBI
Methyl N-(5-thenoyl-2-benzimidazolyl)carbamate	ChEBI
N-(5-(2-Thenoyl)-2-benzimidazolyl)carbamic acid methyl ester	ChEBI
N-(5-(2-Thienoyl)-2-benzimidazolyl)carbamic acid methyl ester	ChEBI
Nocodazol	ChEBI
Nocodazolum	ChEBI
Oncodazole	ChEBI
R 17934	ChEBI
R-17934	ChEBI
R17,934	ChEBI
(5-(2-Thienylcarbonyl)-1H-benzimidazol-2-yl)-carbamate methyl ester	Generator
Methyl (5-(2-thienylcarbonyl))-1H-benzimidazole-2-ylcarbamic acid	Generator
Methyl N-(5-thenoyl-2-benzimidazolyl)carbamic acid	Generator
N-(5-(2-Thenoyl)-2-benzimidazolyl)carbamate methyl ester	Generator
N-(5-(2-Thienoyl)-2-benzimidazolyl)carbamate methyl ester	Generator

Chemical Formula

C₁₄H₁₁N₃O₃S

Average Molecular Weight

301.32

Monoisotopic Molecular Weight

301.052111923

IUPAC Name

methyl N-[6-(thiophene-2-carbonyl)-1H-1,3-benzodiazol-2-yl]carbamate

Traditional Name

nocodazole

CAS Registry Number

Not Available

SMILES

COC(=O)NC1=NC2=CC=C(C=C2N1)C(=O)C1=CC=CS1

InChI Identifier

InChI=1S/C14H11N3O3S/c1-20-14(19)17-13-15-9-5-4-8(7-10(9)16-13)12(18)11-3-2-6-21-11/h2-7H,1H3,(H2,15,16,17,19)

InChI Key

KYRVNWMVYQXFEU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Not Available

Direct Parent

Benzimidazoles

Alternative Parents

Substituents

Benzimidazole
Thiophene carboxylic acid or derivatives
Aryl ketone
Benzenoid
Azole
Imidazole
Thiophene
Heteroaromatic compound
Ketone
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Azacycle
Carboximidic acid derivative
Organopnictogen compound
Organic nitrogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

carbamate ester (CHEBI:34892 )
thiophenes (CHEBI:34892 )
aromatic ketone (CHEBI:34892 )
benzimidazoles (CHEBI:34892 )

Ontology

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	2.84	ALOGPS
logP	3.17	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	8.34	ChemAxon
pKa (Strongest Basic)	3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	84.08 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	78.39 m³·mol⁻¹	ChemAxon
Polarizability	30.93 Å³	ChemAxon
Number of Rings	3	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]+	164.768	30932474
DeepCCS	[M-H]-	162.41	30932474
DeepCCS	[M-2H]-	196.207	30932474
DeepCCS	[M+Na]+	171.36	30932474
AllCCS	[M+H]+	167.1	32859911
AllCCS	[M+H-H2O]+	163.6	32859911
AllCCS	[M+NH4]+	170.4	32859911
AllCCS	[M+Na]+	171.3	32859911
AllCCS	[M-H]-	168.9	32859911
AllCCS	[M+Na-2H]-	168.3	32859911
AllCCS	[M+HCOO]-	167.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Nocodazole	COC(=O)NC1=NC2=CC=C(C=C2N1)C(=O)C1=CC=CS1	3766.8	Standard polar	33892256
Nocodazole	COC(=O)NC1=NC2=CC=C(C=C2N1)C(=O)C1=CC=CS1	2646.9	Standard non polar	33892256
Nocodazole	COC(=O)NC1=NC2=CC=C(C=C2N1)C(=O)C1=CC=CS1	3152.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Nocodazole,1TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C	2829.2	Semi standard non polar	33892256
Nocodazole,1TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C	2767.5	Standard non polar	33892256
Nocodazole,1TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C	4061.8	Standard polar	33892256
Nocodazole,1TMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C	2969.4	Semi standard non polar	33892256
Nocodazole,1TMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C	2783.6	Standard non polar	33892256
Nocodazole,1TMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C	4233.8	Standard polar	33892256
Nocodazole,2TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C)[Si](C)(C)C	2879.4	Semi standard non polar	33892256
Nocodazole,2TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C)[Si](C)(C)C	2752.2	Standard non polar	33892256
Nocodazole,2TMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C)[Si](C)(C)C	3551.0	Standard polar	33892256
Nocodazole,1TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C(C)(C)C	3022.4	Semi standard non polar	33892256
Nocodazole,1TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C(C)(C)C	2963.6	Standard non polar	33892256
Nocodazole,1TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2[NH]1)[Si](C)(C)C(C)(C)C	3983.3	Standard polar	33892256
Nocodazole,1TBDMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C	3151.8	Semi standard non polar	33892256
Nocodazole,1TBDMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C	2986.1	Standard non polar	33892256
Nocodazole,1TBDMS,isomer #2	COC(=O)NC1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C	4150.5	Standard polar	33892256
Nocodazole,2TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3225.3	Semi standard non polar	33892256
Nocodazole,2TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3144.3	Standard non polar	33892256
Nocodazole,2TBDMS,isomer #1	COC(=O)N(C1=NC2=CC=C(C(=O)C3=CC=CS3)C=C2N1[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3566.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Nocodazole GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-1790000000-825534d5d7b658640d20	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Nocodazole GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Nocodazole , positive-QTOF	splash10-00di-3790000000-449c2492c2ab67a70502	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 10V, Positive-QTOF	splash10-0udi-0059000000-32c61dc92bf665194cfd	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 20V, Positive-QTOF	splash10-00kf-0190000000-0b03ee19763aafda8637	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 40V, Positive-QTOF	splash10-0006-1490000000-b138a6f40b2cc9f1c17d	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 10V, Negative-QTOF	splash10-0ldi-4095000000-1acc188f83672b11d1c5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 20V, Negative-QTOF	splash10-014i-4092000000-a97f7670cc206c37f57c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nocodazole 40V, Negative-QTOF	splash10-0a4i-9130000000-c16486ccbe15cf396319	2016-08-03	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

DB08313

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3979

KEGG Compound ID

C13719

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Nocodazole

METLIN ID

Not Available

PubChem Compound

4122

PDB ID

Not Available

ChEBI ID

34892

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 Nocodazole (HMDB0255688)

MOL for HMDB0255688 (Nocodazole)

3D MOL for HMDB0255688 (Nocodazole)

3D SDF for HMDB0255688 (Nocodazole)

3D-SDF for HMDB0255688 (Nocodazole)

PDB for HMDB0255688 (Nocodazole)

3D PDB for HMDB0255688 (Nocodazole)

SMILES for HMDB0255688 (Nocodazole)

INCHI for HMDB0255688 (Nocodazole)

Structure for HMDB0255688 (Nocodazole)

3D Structure for HMDB0255688 (Nocodazole)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra