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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-09 16:13:18 UTC

Update Date

2019-07-23 07:15:36 UTC

HMDB ID

HMDB0061025

Secondary Accession Numbers

HMDB61025

Metabolite Identification

Common Name

5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one

Description

5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 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). 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one is a very strong basic compound (based on its pKa).

Structure

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

HMDB0061025
     RDKit          3D
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one
 31 33  0  0  0  0  0  0  0  0999 V2000
   -0.1461   -1.5351   -2.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7516   -1.1111   -1.8382 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0586   -1.2501   -1.9206 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375   -0.7533   -0.8386 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9320   -0.6366   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2333   -0.0557    0.7971 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9210    0.0757    1.3129 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.2117    0.4180    1.5927 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124    0.2951    1.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6042   -0.2813   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4170   -0.4986   -0.6614 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9127   -0.2150   -0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545   -0.0915    1.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7724   -0.3670    1.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4928    0.3755    0.2616 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7809    1.4430   -0.3611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4736    1.0389   -0.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -1.6471   -2.6702 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7393   -1.0042   -1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4437    0.8762    2.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1132    0.6594    1.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5682   -1.0403   -0.7172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7923   -0.7832    1.8290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2137    0.9903    1.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0410   -0.0509    2.2707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9369   -1.4723    1.1858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1360   -0.1473   -0.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6308    2.2425    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4323    1.8712   -1.1506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5328    0.8158   -2.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7276    1.8392   -0.8024 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  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 11  2  1  0
 17 12  1  0
 10  4  1  0
  1 18  1  0
  5 19  1  0
  8 20  1  0
  9 21  1  0
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 17 31  1  0
M  END


  Mrv0541 07091309132D          

 17 19  0  0  0  0            999 V2000
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769    2.4777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7179    2.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8220    3.2623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4630    2.8207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249    1.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.0150    3.4338    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4699    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11 10  2  0  0  0  0
 13  8  1  0  0  0  0
 14  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15 10  1  0  0  0  0
 15 12  2  0  0  0  0
 16  9  1  0  0  0  0
 16 11  1  0  0  0  0
 16 12  1  0  0  0  0
 17 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061025

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=NC2=C(C=CC(Cl)=C2)N1C1CCNCC1

> <INCHI_IDENTIFIER>
InChI=1S/C12H14ClN3O/c13-8-1-2-11-10(7-8)15-12(17)16(11)9-3-5-14-6-4-9/h1-2,7,9,14H,3-6H2,(H,15,17)

> <INCHI_KEY>
DOAYWDKFDPSTSV-UHFFFAOYSA-N

> <FORMULA>
C12H14ClN3O

> <MOLECULAR_WEIGHT>
251.712

> <EXACT_MASS>
251.082539792

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
26.17782745322147

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-chloro-1-(piperidin-4-yl)-1H-1,3-benzodiazol-2-ol

> <ALOGPS_LOGP>
2.05

> <JCHEM_LOGP>
2.111667614

> <ALOGPS_LOGS>
-2.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.672088851335971

> <JCHEM_PKA_STRONGEST_BASIC>
10.126027570191779

> <JCHEM_POLAR_SURFACE_AREA>
50.08

> <JCHEM_REFRACTIVITY>
66.2806

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.57e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-chloro-1-(piperidin-4-yl)-1,3-benzodiazol-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0061025
     RDKit          3D
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one
 31 33  0  0  0  0  0  0  0  0999 V2000
   -0.1461   -1.5351   -2.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7516   -1.1111   -1.8382 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0586   -1.2501   -1.9206 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375   -0.7533   -0.8386 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9320   -0.6366   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2333   -0.0557    0.7971 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9210    0.0757    1.3129 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.2117    0.4180    1.5927 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124    0.2951    1.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6042   -0.2813   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4170   -0.4986   -0.6614 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9127   -0.2150   -0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545   -0.0915    1.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7724   -0.3670    1.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4928    0.3755    0.2616 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7809    1.4430   -0.3611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4736    1.0389   -0.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -1.6471   -2.6702 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7393   -1.0042   -1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4437    0.8762    2.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1132    0.6594    1.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5682   -1.0403   -0.7172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7923   -0.7832    1.8290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2137    0.9903    1.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0410   -0.0509    2.2707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9369   -1.4723    1.1858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1360   -0.1473   -0.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6308    2.2425    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4323    1.8712   -1.1506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5328    0.8158   -2.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7276    1.8392   -0.8024 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  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 11  2  1  0
 17 12  1  0
 10  4  1  0
  1 18  1  0
  5 19  1  0
  8 20  1  0
  9 21  1  0
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 17 31  1  0
M  END

HEADER    PROTEIN                                 09-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-13         0                                  
HETATM    1  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.877   4.625   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.340   3.801   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.401   6.090   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.864   5.265   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0       8.788  -0.770   0.000  0.00  0.00          Cl+0
HETATM   14  N   UNK     0       1.895   6.410   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       0.877   0.770   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1   11                                                       
CONECT    3    5    9                                                       
CONECT    4    6    9                                                       
CONECT    5    3   14                                                       
CONECT    6    4   14                                                       
CONECT    7    8   10                                                       
CONECT    8    1    7   13                                                  
CONECT    9    3    4   16                                                  
CONECT   10    7   11   15                                                  
CONECT   11    2   10   16                                                  
CONECT   12   15   16   17                                                  
CONECT   13    8                                                            
CONECT   14    5    6                                                       
CONECT   15   10   12                                                       
CONECT   16    9   11   12                                                  
CONECT   17   12                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0061025
HETATM    1  O1  UNL     1      -0.146  -1.535  -2.822  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.752  -1.111  -1.838  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.059  -1.250  -1.921  1.00  0.00           N  
HETATM    4  C2  UNL     1       2.638  -0.753  -0.839  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.932  -0.637  -0.411  1.00  0.00           C  
HETATM    6  C4  UNL     1       4.233  -0.056   0.797  1.00  0.00           C  
HETATM    7 CL1  UNL     1       5.921   0.076   1.313  1.00  0.00          CL  
HETATM    8  C5  UNL     1       3.212   0.418   1.593  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.912   0.295   1.152  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.604  -0.281  -0.048  1.00  0.00           C  
HETATM   11  N2  UNL     1       0.417  -0.499  -0.661  1.00  0.00           N  
HETATM   12  C8  UNL     1      -0.913  -0.215  -0.292  1.00  0.00           C  
HETATM   13  C9  UNL     1      -1.254  -0.091   1.132  1.00  0.00           C  
HETATM   14  C10 UNL     1      -2.772  -0.367   1.241  1.00  0.00           C  
HETATM   15  N3  UNL     1      -3.493   0.376   0.262  1.00  0.00           N  
HETATM   16  C11 UNL     1      -2.781   1.443  -0.361  1.00  0.00           C  
HETATM   17  C12 UNL     1      -1.474   1.039  -0.984  1.00  0.00           C  
HETATM   18  H1  UNL     1      -1.131  -1.647  -2.670  1.00  0.00           H  
HETATM   19  H2  UNL     1       4.739  -1.004  -1.026  1.00  0.00           H  
HETATM   20  H3  UNL     1       3.444   0.876   2.545  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.113   0.659   1.761  1.00  0.00           H  
HETATM   22  H5  UNL     1      -1.568  -1.040  -0.717  1.00  0.00           H  
HETATM   23  H6  UNL     1      -0.792  -0.783   1.829  1.00  0.00           H  
HETATM   24  H7  UNL     1      -1.214   0.990   1.450  1.00  0.00           H  
HETATM   25  H8  UNL     1      -3.041  -0.051   2.271  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.937  -1.472   1.186  1.00  0.00           H  
HETATM   27  H10 UNL     1      -4.136  -0.147  -0.328  1.00  0.00           H  
HETATM   28  H11 UNL     1      -2.631   2.243   0.397  1.00  0.00           H  
HETATM   29  H12 UNL     1      -3.432   1.871  -1.151  1.00  0.00           H  
HETATM   30  H13 UNL     1      -1.533   0.816  -2.054  1.00  0.00           H  
HETATM   31  H14 UNL     1      -0.728   1.839  -0.802  1.00  0.00           H  
CONECT    1    2   18
CONECT    2    3    3   11
CONECT    3    4
CONECT    4    5    5   10
CONECT    5    6   19
CONECT    6    7    8    8
CONECT    8    9   20
CONECT    9   10   10   21
CONECT   10   11
CONECT   11   12
CONECT   12   13   17   22
CONECT   13   14   23   24
CONECT   14   15   25   26
CONECT   15   16   27
CONECT   16   17   28   29
CONECT   17   30   31
END

HMDB0061025
     RDKit          3D
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one
 31 33  0  0  0  0  0  0  0  0999 V2000
   -0.1461   -1.5351   -2.8224 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7516   -1.1111   -1.8382 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0586   -1.2501   -1.9206 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375   -0.7533   -0.8386 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9320   -0.6366   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2333   -0.0557    0.7971 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9210    0.0757    1.3129 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.2117    0.4180    1.5927 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9124    0.2951    1.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6042   -0.2813   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4170   -0.4986   -0.6614 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9127   -0.2150   -0.2919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545   -0.0915    1.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7724   -0.3670    1.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4928    0.3755    0.2616 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7809    1.4430   -0.3611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4736    1.0389   -0.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -1.6471   -2.6702 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7393   -1.0042   -1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4437    0.8762    2.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1132    0.6594    1.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5682   -1.0403   -0.7172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7923   -0.7832    1.8290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2137    0.9903    1.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0410   -0.0509    2.2707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9369   -1.4723    1.1858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1360   -0.1473   -0.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6308    2.2425    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4323    1.8712   -1.1506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5328    0.8158   -2.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7276    1.8392   -0.8024 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  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 11  2  1  0
 17 12  1  0
 10  4  1  0
  1 18  1  0
  5 19  1  0
  8 20  1  0
  9 21  1  0
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
 14 26  1  0
 15 27  1  0
 16 28  1  0
 16 29  1  0
 17 30  1  0
 17 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₂H₁₄ClN₃O

Average Molecular Weight

251.712

Monoisotopic Molecular Weight

251.082539792

IUPAC Name

5-chloro-1-(piperidin-4-yl)-1H-1,3-benzodiazol-2-ol

Traditional Name

5-chloro-1-(piperidin-4-yl)-1,3-benzodiazol-2-ol

CAS Registry Number

Not Available

SMILES

OC1=NC2=C(C=CC(Cl)=C2)N1C1CCNCC1

InChI Identifier

InChI=1S/C12H14ClN3O/c13-8-1-2-11-10(7-8)15-12(17)16(11)9-3-5-14-6-4-9/h1-2,7,9,14H,3-6H2,(H,15,17)

InChI Key

DOAYWDKFDPSTSV-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
Aryl chloride
Aryl halide
N-substituted imidazole
Benzenoid
Piperidine
Azole
Imidazole
Heteroaromatic compound
Urea
Secondary aliphatic amine
Azacycle
Secondary amine
Organochloride
Organohalogen compound
Hydrocarbon derivative
Amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Kidney (HMDB: HMDB0061025)
Liver (HMDB: HMDB0061025)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0061025)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0061025)

Cellular substructure

Cytoplasm (HMDB: HMDB0061025)
Membrane (HMDB: HMDB0061025)

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
Water Solubility	0.66 g/L	ALOGPS
logP	2.05	ALOGPS
logP	2.11	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	12.67	ChemAxon
pKa (Strongest Basic)	10.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	50.08 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	66.28 m³·mol⁻¹	ChemAxon
Polarizability	26.18 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]+	152.638	30932474
DeepCCS	[M-H]-	150.243	30932474
DeepCCS	[M-2H]-	183.783	30932474
DeepCCS	[M+Na]+	158.576	30932474
AllCCS	[M+H]+	156.4	32859911
AllCCS	[M+H-H2O]+	152.6	32859911
AllCCS	[M+NH4]+	159.9	32859911
AllCCS	[M+Na]+	160.9	32859911
AllCCS	[M-H]-	157.6	32859911
AllCCS	[M+Na-2H]-	157.5	32859911
AllCCS	[M+HCOO]-	157.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one	OC1=NC2=C(C=CC(Cl)=C2)N1C1CCNCC1	2990.5	Standard polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one	OC1=NC2=C(C=CC(Cl)=C2)N1C1CCNCC1	2285.0	Standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one	OC1=NC2=C(C=CC(Cl)=C2)N1C1CCNCC1	2550.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,1TMS,isomer #1	C[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCNCC1	2295.8	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,1TMS,isomer #2	C[Si](C)(C)N1CCC(N2C(O)=NC3=CC(Cl)=CC=C32)CC1	2572.5	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TMS,isomer #1	C[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C)CC1	2497.5	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TMS,isomer #1	C[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C)CC1	2229.2	Standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TMS,isomer #1	C[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C)CC1	2960.3	Standard polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCNCC1	2476.3	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1CCC(N2C(O)=NC3=CC(Cl)=CC=C32)CC1	2749.1	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C(C)(C)C)CC1	2846.8	Semi standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C(C)(C)C)CC1	2636.6	Standard non polar	33892256
5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NC2=CC(Cl)=CC=C2N1C1CCN([Si](C)(C)C(C)(C)C)CC1	3129.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-05ai-8490000000-3f8b681d744f7a045480	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one GC-MS (1 TMS) - 70eV, Positive	splash10-05gi-9061000000-d2a7dff424f196689ea4	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 10V, Positive-QTOF	splash10-0udi-0090000000-9d469a9fa899f03251b4	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 20V, Positive-QTOF	splash10-0udi-1190000000-20e0617678c42c685286	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 40V, Positive-QTOF	splash10-00lr-8920000000-1b26e98eb29ac190121a	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 10V, Negative-QTOF	splash10-0udi-0090000000-370178c7d470291d36d0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 20V, Negative-QTOF	splash10-0udi-1390000000-6975d4d15635ab98d6d4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 40V, Negative-QTOF	splash10-0159-1900000000-937ceb8cc5597374fb8a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 10V, Positive-QTOF	splash10-0udi-0090000000-58ce7c4dc6da17c9a7a4	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 20V, Positive-QTOF	splash10-0zfr-0090000000-0245af6af638caed2cf2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 40V, Positive-QTOF	splash10-06si-9670000000-70bfd6d521553cd1ad4d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 10V, Negative-QTOF	splash10-0udi-0090000000-04e42f2a5f5ba9ac5bb2	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 20V, Negative-QTOF	splash10-0udi-2090000000-733cf492dbf121072419	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one 40V, Negative-QTOF	splash10-001r-5900000000-fcf82d4a96af79cb2bac	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

104607

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

Not Available

Showing metabocard for 5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one (HMDB0061025)

MOL for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

3D MOL for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

3D SDF for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

3D-SDF for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

PDB for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

3D PDB for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

SMILES for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

INCHI for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

Structure for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

3D Structure for HMDB0061025 (5-Chloro-1,3-dihydro-1-(4-piperidinyl)-2H-benzimidazol-2-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra