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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 03:24:38 UTC

Update Date

2021-09-26 22:59:31 UTC

HMDB ID

HMDB0248945

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Bendamustine

Description

Bendamustine, also known as treanda, 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 very few articles have been published on Bendamustine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Bendamustine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Bendamustine 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

HMDB0248945
     RDKit          3D
Bendamustine
 44 45  0  0  0  0  0  0  0  0999 V2000
    2.0834    0.1213   -3.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5370   -0.2059   -1.7452 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -0.7984   -0.7512 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6458   -1.2240   -0.7953 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6065   -0.1841   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4973    0.3479    1.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6425   -0.5834    2.1030 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8533   -1.8169    2.0339 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.0843    3.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3461   -0.9170    0.2623 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1506   -0.4129   -0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877   -0.2676    0.5279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1506    0.3131   -0.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4382    0.4871    0.4443 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7309    1.6644    1.2097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9251    1.2932    2.6582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2818    2.8131    3.5362 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4631   -0.5169    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9487   -1.6746   -0.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2305   -2.8877   -0.7991 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.9910    0.7645   -1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7810    0.6312   -2.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2603    0.0501   -1.3856 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3370   -0.7859   -3.6233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9858    0.7951   -2.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3606    0.6917   -3.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7910   -2.2108   -0.3015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8963   -1.4359   -1.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6369   -0.6434   -0.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    0.6254   -1.1388 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4892    0.8412    1.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2274    1.1849    1.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1794    0.8366    3.6044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2330   -0.6113    1.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6797    2.1265    0.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9335    2.4314    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9847    0.8947    3.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7795    0.5818    2.7612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3884   -0.1104   -0.1643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7048   -0.9237    1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0780   -2.0954   -0.0268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5949   -1.3082   -1.5615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8252    1.2210   -1.9490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6660    0.9823   -3.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  3 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 14 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  2  0
 21 22  1  0
 22 23  2  0
 23  2  1  0
 23 11  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  9 33  1  0
 12 34  1  0
 15 35  1  0
 15 36  1  0
 16 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 19 41  1  0
 19 42  1  0
 21 43  1  0
 22 44  1  0
M  END

  Mrv0541 03151312232D          

 23 24  0  0  0  0            999 V2000
   14.0800   -3.9325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3655   -3.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3655   -2.6950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7945   -3.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7945   -2.6950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0800   -2.2825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5791   -2.4401    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0640   -3.1076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5791   -3.7750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8890   -3.1076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3015   -2.3931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1265   -2.3931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5390   -1.6787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8245   -1.2662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3640   -1.6787    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9916   -1.7257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6511   -3.9325    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6511   -4.7575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9366   -3.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2221   -3.9325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5076   -3.5200    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   11.9366   -5.1700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9366   -5.9950    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  1  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  3  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9  4  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
  7 16  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 18 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248945

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(CCCC(O)=O)=NC2=CC(=CC=C12)N(CCCl)CCCl

> <INCHI_IDENTIFIER>
InChI=1S/C16H21Cl2N3O2/c1-20-14-6-5-12(21(9-7-17)10-8-18)11-13(14)19-15(20)3-2-4-16(22)23/h5-6,11H,2-4,7-10H2,1H3,(H,22,23)

> <INCHI_KEY>
YTKUWDBFDASYHO-UHFFFAOYSA-N

> <FORMULA>
C16H21Cl2N3O2

> <MOLECULAR_WEIGHT>
358.263

> <EXACT_MASS>
357.101082345

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
38.193394007129754

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{5-[bis(2-chloroethyl)amino]-1-methyl-1H-1,3-benzodiazol-2-yl}butanoic acid

> <ALOGPS_LOGP>
3.07

> <JCHEM_LOGP>
1.6649948628935591

> <ALOGPS_LOGS>
-3.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.377239503830114

> <JCHEM_PKA_STRONGEST_BASIC>
6.648069076034413

> <JCHEM_POLAR_SURFACE_AREA>
58.36000000000001

> <JCHEM_REFRACTIVITY>
92.91539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.18e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bendamustine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0248945
     RDKit          3D
Bendamustine
 44 45  0  0  0  0  0  0  0  0999 V2000
    2.0834    0.1213   -3.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5370   -0.2059   -1.7452 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -0.7984   -0.7512 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6458   -1.2240   -0.7953 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6065   -0.1841   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4973    0.3479    1.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6425   -0.5834    2.1030 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8533   -1.8169    2.0339 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.0843    3.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3461   -0.9170    0.2623 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1506   -0.4129   -0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877   -0.2676    0.5279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1506    0.3131   -0.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4382    0.4871    0.4443 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7309    1.6644    1.2097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9251    1.2932    2.6582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2818    2.8131    3.5362 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4631   -0.5169    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9487   -1.6746   -0.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2305   -2.8877   -0.7991 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.9910    0.7645   -1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7810    0.6312   -2.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2603    0.0501   -1.3856 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3370   -0.7859   -3.6233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9858    0.7951   -2.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3606    0.6917   -3.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7910   -2.2108   -0.3015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8963   -1.4359   -1.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6369   -0.6434   -0.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    0.6254   -1.1388 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4892    0.8412    1.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2274    1.1849    1.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1794    0.8366    3.6044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2330   -0.6113    1.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6797    2.1265    0.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9335    2.4314    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9847    0.8947    3.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7795    0.5818    2.7612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3884   -0.1104   -0.1643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7048   -0.9237    1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0780   -2.0954   -0.0268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5949   -1.3082   -1.5615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8252    1.2210   -1.9490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6660    0.9823   -3.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  3 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 14 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  2  0
 21 22  1  0
 22 23  2  0
 23  2  1  0
 23 11  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  9 33  1  0
 12 34  1  0
 15 35  1  0
 15 36  1  0
 16 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 19 41  1  0
 19 42  1  0
 21 43  1  0
 22 44  1  0
M  END

HEADER    PROTEIN                                 15-MAR-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAR-13         0                                  
HETATM    1  C   UNK     0      26.283  -7.341   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.949  -6.571   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      24.949  -5.031   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.616  -6.571   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.616  -5.031   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.283  -4.261   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      29.081  -4.555   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      29.986  -5.801   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      29.081  -7.047   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      31.526  -5.801   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      32.296  -4.467   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      33.836  -4.467   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      34.606  -3.134   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      33.272  -2.364   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      36.146  -3.134   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      29.851  -3.221   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      23.615  -7.341   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      23.615  -8.881   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      22.282  -6.571   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      20.948  -7.341   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0      19.614  -6.571   0.000  0.00  0.00          Cl+0
HETATM   22  C   UNK     0      22.282  -9.651   0.000  0.00  0.00           C+0
HETATM   23 Cl   UNK     0      22.282 -11.191   0.000  0.00  0.00          Cl+0
CONECT    1    2    4                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2    6                                                       
CONECT    4    1    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    3                                                       
CONECT    7    5    8   16                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    7                                                            
CONECT   17    2   18   19                                                  
CONECT   18   17   22                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   18   23                                                       
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0248945
HETATM    1  C1  UNL     1       2.083   0.121  -3.039  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.537  -0.206  -1.745  1.00  0.00           N  
HETATM    3  C2  UNL     1       2.222  -0.798  -0.751  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.646  -1.224  -0.795  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.607  -0.184  -0.362  1.00  0.00           C  
HETATM    6  C5  UNL     1       4.497   0.348   1.001  1.00  0.00           C  
HETATM    7  C6  UNL     1       4.642  -0.583   2.103  1.00  0.00           C  
HETATM    8  O1  UNL     1       4.853  -1.817   2.034  1.00  0.00           O  
HETATM    9  O2  UNL     1       4.541  -0.084   3.397  1.00  0.00           O  
HETATM   10  N2  UNL     1       1.346  -0.917   0.262  1.00  0.00           N  
HETATM   11  C7  UNL     1       0.151  -0.413  -0.090  1.00  0.00           C  
HETATM   12  C8  UNL     1      -1.088  -0.268   0.528  1.00  0.00           C  
HETATM   13  C9  UNL     1      -2.151   0.313  -0.130  1.00  0.00           C  
HETATM   14  N3  UNL     1      -3.438   0.487   0.444  1.00  0.00           N  
HETATM   15  C10 UNL     1      -3.731   1.664   1.210  1.00  0.00           C  
HETATM   16  C11 UNL     1      -3.925   1.293   2.658  1.00  0.00           C  
HETATM   17 CL1  UNL     1      -4.282   2.813   3.536  1.00  0.00          CL  
HETATM   18  C12 UNL     1      -4.463  -0.517   0.258  1.00  0.00           C  
HETATM   19  C13 UNL     1      -3.949  -1.675  -0.585  1.00  0.00           C  
HETATM   20 CL2  UNL     1      -5.231  -2.888  -0.799  1.00  0.00          CL  
HETATM   21  C14 UNL     1      -1.991   0.765  -1.435  1.00  0.00           C  
HETATM   22  C15 UNL     1      -0.781   0.631  -2.062  1.00  0.00           C  
HETATM   23  C16 UNL     1       0.260   0.050  -1.386  1.00  0.00           C  
HETATM   24  H1  UNL     1       2.337  -0.786  -3.623  1.00  0.00           H  
HETATM   25  H2  UNL     1       2.986   0.795  -2.965  1.00  0.00           H  
HETATM   26  H3  UNL     1       1.361   0.692  -3.655  1.00  0.00           H  
HETATM   27  H4  UNL     1       3.791  -2.211  -0.301  1.00  0.00           H  
HETATM   28  H5  UNL     1       3.896  -1.436  -1.881  1.00  0.00           H  
HETATM   29  H6  UNL     1       5.637  -0.643  -0.469  1.00  0.00           H  
HETATM   30  H7  UNL     1       4.608   0.625  -1.139  1.00  0.00           H  
HETATM   31  H8  UNL     1       3.489   0.841   1.110  1.00  0.00           H  
HETATM   32  H9  UNL     1       5.227   1.185   1.176  1.00  0.00           H  
HETATM   33  H10 UNL     1       4.179   0.837   3.604  1.00  0.00           H  
HETATM   34  H11 UNL     1      -1.233  -0.611   1.540  1.00  0.00           H  
HETATM   35  H12 UNL     1      -4.680   2.126   0.856  1.00  0.00           H  
HETATM   36  H13 UNL     1      -2.934   2.431   1.149  1.00  0.00           H  
HETATM   37  H14 UNL     1      -2.985   0.895   3.098  1.00  0.00           H  
HETATM   38  H15 UNL     1      -4.780   0.582   2.761  1.00  0.00           H  
HETATM   39  H16 UNL     1      -5.388  -0.110  -0.164  1.00  0.00           H  
HETATM   40  H17 UNL     1      -4.705  -0.924   1.257  1.00  0.00           H  
HETATM   41  H18 UNL     1      -3.078  -2.095  -0.027  1.00  0.00           H  
HETATM   42  H19 UNL     1      -3.595  -1.308  -1.561  1.00  0.00           H  
HETATM   43  H20 UNL     1      -2.825   1.221  -1.949  1.00  0.00           H  
HETATM   44  H21 UNL     1      -0.666   0.982  -3.067  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3   23
CONECT    3    4   10   10
CONECT    4    5   27   28
CONECT    5    6   29   30
CONECT    6    7   31   32
CONECT    7    8    8    9
CONECT    9   33
CONECT   10   11
CONECT   11   12   12   23
CONECT   12   13   34
CONECT   13   14   21   21
CONECT   14   15   18
CONECT   15   16   35   36
CONECT   16   17   37   38
CONECT   18   19   39   40
CONECT   19   20   41   42
CONECT   21   22   43
CONECT   22   23   23   44
END

HMDB0248945
     RDKit          3D
Bendamustine
 44 45  0  0  0  0  0  0  0  0999 V2000
    2.0834    0.1213   -3.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5370   -0.2059   -1.7452 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -0.7984   -0.7512 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6458   -1.2240   -0.7953 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6065   -0.1841   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4973    0.3479    1.0014 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6425   -0.5834    2.1030 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8533   -1.8169    2.0339 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5408   -0.0843    3.3972 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3461   -0.9170    0.2623 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1506   -0.4129   -0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877   -0.2676    0.5279 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1506    0.3131   -0.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4382    0.4871    0.4443 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7309    1.6644    1.2097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9251    1.2932    2.6582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2818    2.8131    3.5362 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.4631   -0.5169    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9487   -1.6746   -0.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2305   -2.8877   -0.7991 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.9910    0.7645   -1.4353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7810    0.6312   -2.0622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2603    0.0501   -1.3856 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3370   -0.7859   -3.6233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9858    0.7951   -2.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3606    0.6917   -3.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7910   -2.2108   -0.3015 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8963   -1.4359   -1.8812 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6369   -0.6434   -0.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    0.6254   -1.1388 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4892    0.8412    1.1103 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2274    1.1849    1.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1794    0.8366    3.6044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2330   -0.6113    1.5400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6797    2.1265    0.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9335    2.4314    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9847    0.8947    3.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7795    0.5818    2.7612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3884   -0.1104   -0.1643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7048   -0.9237    1.2565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0780   -2.0954   -0.0268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5949   -1.3082   -1.5615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8252    1.2210   -1.9490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6660    0.9823   -3.0672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  3 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 14 18  1  0
 18 19  1  0
 19 20  1  0
 13 21  2  0
 21 22  1  0
 22 23  2  0
 23  2  1  0
 23 11  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  9 33  1  0
 12 34  1  0
 15 35  1  0
 15 36  1  0
 16 37  1  0
 16 38  1  0
 18 39  1  0
 18 40  1  0
 19 41  1  0
 19 42  1  0
 21 43  1  0
 22 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Treanda	Kegg
Bendamustin	MeSH
Cytostasan	MeSH
Hydrochloride, bendamustine	MeSH
Zimet 3393	MeSH
Bendamustine hydrochloride	MeSH
IMET 3393	MeSH
Ribomustin	MeSH
4-{5-[bis(2-chloroethyl)amino]-1-methyl-1H-1,3-benzodiazol-2-yl}butanoate	Generator

Chemical Formula

C₁₆H₂₁Cl₂N₃O₂

Average Molecular Weight

358.263

Monoisotopic Molecular Weight

357.101082345

IUPAC Name

4-{5-[bis(2-chloroethyl)amino]-1-methyl-1H-1,3-benzodiazol-2-yl}butanoic acid

Traditional Name

bendamustine

CAS Registry Number

Not Available

SMILES

CN1C(CCCC(O)=O)=NC2=CC(=CC=C12)N(CCCl)CCCl

InChI Identifier

InChI=1S/C16H21Cl2N3O2/c1-20-14-6-5-12(21(9-7-17)10-8-18)11-13(14)19-15(20)3-2-4-16(22)23/h5-6,11H,2-4,7-10H2,1H3,(H,22,23)

InChI Key

YTKUWDBFDASYHO-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
Dialkylarylamine
Tertiary aliphatic/aromatic amine
Nitrogen mustard
Benzenoid
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Amino acid or derivatives
Amino acid
Tertiary amine
Carboxylic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Alkyl chloride
Organohalogen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Alkyl halide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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: HMDB0248945)

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	3.07	ALOGPS
logP	1.66	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	4.38	ChemAxon
pKa (Strongest Basic)	6.65	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	58.36 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	92.92 m³·mol⁻¹	ChemAxon
Polarizability	38.19 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-2H]-	207.72	30932474
DeepCCS	[M+Na]+	183.286	30932474
AllCCS	[M+H]+	178.4	32859911
AllCCS	[M+H-H2O]+	175.7	32859911
AllCCS	[M+NH4]+	180.7	32859911
AllCCS	[M+Na]+	181.4	32859911
AllCCS	[M-H]-	179.8	32859911
AllCCS	[M+Na-2H]-	180.0	32859911
AllCCS	[M+HCOO]-	180.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Bendamustine	CN1C(CCCC(O)=O)=NC2=CC(=CC=C12)N(CCCl)CCCl	3885.0	Standard polar	33892256
Bendamustine	CN1C(CCCC(O)=O)=NC2=CC(=CC=C12)N(CCCl)CCCl	2861.1	Standard non polar	33892256
Bendamustine	CN1C(CCCC(O)=O)=NC2=CC(=CC=C12)N(CCCl)CCCl	3191.7	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 - Bendamustine GC-MS (Non-derivatized) - 70eV, Positive	splash10-007p-1191000000-105ac77aa88dc5f6e5f6	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bendamustine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bendamustine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bendamustine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	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 - Bendamustine 10V, Positive-QTOF	splash10-0a4l-0019000000-0f818e01f361056a0d0c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 20V, Positive-QTOF	splash10-03di-2269000000-c192408ea9a9e85da7cd	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 40V, Positive-QTOF	splash10-0nti-4490000000-ceed33c0d499c0f77ed1	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 10V, Negative-QTOF	splash10-0a4i-0019000000-0240751349662f6372f8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 20V, Negative-QTOF	splash10-0ab9-1059000000-3a032820e05c6eab1ea4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 40V, Negative-QTOF	splash10-0a4l-9180000000-1a2593c3241828530387	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 10V, Positive-QTOF	splash10-0a4l-0009000000-f4a949918cc4801f4f62	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 20V, Positive-QTOF	splash10-0kp3-0095000000-611f1776a238691ca2dd	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 40V, Positive-QTOF	splash10-0udl-3190000000-fcbcddad210bb67dfa8c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 10V, Negative-QTOF	splash10-001i-9002000000-e3c3fcad2466ad25dd43	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 20V, Negative-QTOF	splash10-001i-9000000000-c2fa753da65a4bac80a1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bendamustine 40V, Negative-QTOF	splash10-001i-9001000000-1e0a0a41fab832cd88b2	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

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

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB06769

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

59069

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Bendamustine

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 Bendamustine (HMDB0248945)

MOL for HMDB0248945 (Bendamustine)

3D MOL for HMDB0248945 (Bendamustine)

3D SDF for HMDB0248945 (Bendamustine)

3D-SDF for HMDB0248945 (Bendamustine)

PDB for HMDB0248945 (Bendamustine)

3D PDB for HMDB0248945 (Bendamustine)

SMILES for HMDB0248945 (Bendamustine)

INCHI for HMDB0248945 (Bendamustine)

Structure for HMDB0248945 (Bendamustine)

3D Structure for HMDB0248945 (Bendamustine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra