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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 00:52:35 UTC

Update Date

2021-09-26 22:57:37 UTC

HMDB ID

HMDB0247749

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Abemaciclib

Description

Abemaciclib 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 Abemaciclib. This compound has been identified in human blood as reported by (PMID: 31557052 ). Abemaciclib is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Abemaciclib 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


  Mrv1652310201623092D          

 37 41  0  0  0  0            999 V2000
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M  END

HMDB0247749
     RDKit          3D
Abemaciclib
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M  END


  Mrv1652310201623092D          

 37 41  0  0  0  0            999 V2000
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 23 28  2  0  0  0  0
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 26 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 25 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 31 36  1  0  0  0  0
 20 37  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247749

> <DATABASE_NAME>
hmdb

> <SMILES>
CCN1CCN(CC2=CC=C(NC3=NC=C(F)C(=N3)C3=CC(F)=C4N=C(C)N(C(C)C)C4=C3)N=C2)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C27H32F2N8/c1-5-35-8-10-36(11-9-35)16-19-6-7-24(30-14-19)33-27-31-15-22(29)25(34-27)20-12-21(28)26-23(13-20)37(17(2)3)18(4)32-26/h6-7,12-15,17H,5,8-11,16H2,1-4H3,(H,30,31,33,34)

> <INCHI_KEY>
UZWDCWONPYILKI-UHFFFAOYSA-N

> <FORMULA>
C27H32F2N8

> <MOLECULAR_WEIGHT>
506.606

> <EXACT_MASS>
506.271799388

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
54.746005320074296

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzodiazol-6-yl]pyrimidin-2-amine

> <ALOGPS_LOGP>
4.25

> <JCHEM_LOGP>
4.415418176

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.272513702818289

> <JCHEM_PKA_STRONGEST_BASIC>
7.944466948303721

> <JCHEM_POLAR_SURFACE_AREA>
75.0

> <JCHEM_REFRACTIVITY>
141.26479999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.59e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-(7-fluoro-3-isopropyl-2-methyl-1,3-benzodiazol-5-yl)pyrimidin-2-amine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0247749
     RDKit          3D
Abemaciclib
 69 73  0  0  0  0  0  0  0  0999 V2000
    8.3651   -2.8084    1.4473 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6308   -1.3439    1.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7777   -0.6974    0.3393 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1031    0.7013    0.2724 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3814    1.5285    1.2861 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9387    1.3593    1.2023 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4876    1.6932   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0150    1.5691   -0.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3702    1.3085   -1.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9607    1.2051   -1.4346 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107    1.3599   -0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1777    1.2645   -0.2995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0557    1.0113   -1.3612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6228    0.8146   -2.6114 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4770    0.5752   -3.6053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8504    0.5286   -3.3371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609    0.2809   -4.3929 F   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3160    0.7289   -2.0547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7485    0.6750   -1.8021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6269    1.3198   -2.6484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9875    1.2699   -2.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8884    1.9005   -3.2336 F   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5116    0.5749   -1.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7682    0.3796   -0.8823 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6884   -0.3807    0.2307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8314   -0.8642    1.0818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3913   -0.6640    0.4929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8418   -1.4458    1.5812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8788   -0.6389    2.4340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2347   -2.7392    1.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6384   -0.0719   -0.4718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2781   -0.0151   -0.7194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4139    0.9645   -1.1002 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8892    1.6183    0.8612 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2198    1.7188    0.9101 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6887   -0.0462    1.4810 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3874   -0.9669    0.5086 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3224   -3.3107    1.7139 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0430   -3.2684    0.4762 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6559   -3.0505    2.2655 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6825   -1.2355    0.9099 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5625   -0.8476    2.2929 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9684    1.0517   -0.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2045    0.7785    0.4816 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7367    1.3151    2.2983 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6050    2.5942    1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7820    2.7302   -0.3556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9363    1.0460   -0.9136 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9348    1.1809   -2.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5324    0.9977   -2.4114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6440    1.4062    0.6578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    0.4164   -4.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2779    1.8835   -3.5226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7681   -1.9744    1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8653   -0.3706    2.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7632   -0.6958    0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6994   -1.7132    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7767    0.4060    2.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1998   -0.5834    3.4948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8783   -1.1607    2.4590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2982   -3.4585    1.9701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8666   -3.1366    0.2984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1873   -2.6694    0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6074   -0.5135   -0.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7207    1.9293    1.8658 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9869   -0.2396    2.5244 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6102   -0.2357    1.3823 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8678   -0.9425   -0.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2587   -1.9969    0.8991 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  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 28 29  1  0
 28 30  1  0
 27 31  1  0
 31 32  2  0
 18 33  2  0
 11 34  1  0
 34 35  2  0
  6 36  1  0
 36 37  1  0
 37  3  1  0
 35  8  1  0
 33 13  1  0
 32 19  1  0
 31 23  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  2 41  1  0
  2 42  1  0
  4 43  1  0
  4 44  1  0
  5 45  1  0
  5 46  1  0
  7 47  1  0
  7 48  1  0
  9 49  1  0
 10 50  1  0
 12 51  1  0
 15 52  1  0
 20 53  1  0
 26 54  1  0
 26 55  1  0
 26 56  1  0
 28 57  1  0
 29 58  1  0
 29 59  1  0
 29 60  1  0
 30 61  1  0
 30 62  1  0
 30 63  1  0
 32 64  1  0
 35 65  1  0
 36 66  1  0
 36 67  1  0
 37 68  1  0
 37 69  1  0
M  END

HEADER    PROTEIN                                 20-OCT-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-OCT-16         0                                  
HETATM    1  C   UNK     0      19.868   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.868   2.073   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      18.535   1.303   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      18.535  -0.237   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.201  -1.007   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      15.867  -0.237   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      15.867   1.303   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      17.201   2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.534  -1.007   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.200  -0.237   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.866  -1.007   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.533  -0.237   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.533   1.303   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      11.866   2.073   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      13.200   1.303   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       9.199   2.073   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       7.865   1.303   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       7.865  -0.237   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       6.531  -1.007   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.198  -0.237   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.198   1.303   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       6.531   2.073   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM   29  F   UNK     0       2.530   5.923   0.000  0.00  0.00           F+0
HETATM   30  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      -0.744   0.132   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.287  -1.012   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.250  -0.188   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.713   2.843   0.000  0.00  0.00           C+0
HETATM   37  F   UNK     0       3.864  -1.007   0.000  0.00  0.00           F+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    6   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16   13   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   37                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21   17                                                       
CONECT   23   21   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   27   30                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   23                                                       
CONECT   29   27                                                            
CONECT   30   26   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   25   33                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   31                                                            
CONECT   37   20                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

COMPND    HMDB0247749
HETATM    1  C1  UNL     1       8.365  -2.808   1.447  1.00  0.00           C  
HETATM    2  C2  UNL     1       8.631  -1.344   1.307  1.00  0.00           C  
HETATM    3  N1  UNL     1       7.778  -0.697   0.339  1.00  0.00           N  
HETATM    4  C3  UNL     1       8.103   0.701   0.272  1.00  0.00           C  
HETATM    5  C4  UNL     1       7.381   1.529   1.286  1.00  0.00           C  
HETATM    6  N2  UNL     1       5.939   1.359   1.202  1.00  0.00           N  
HETATM    7  C5  UNL     1       5.488   1.693  -0.136  1.00  0.00           C  
HETATM    8  C6  UNL     1       4.015   1.569  -0.212  1.00  0.00           C  
HETATM    9  C7  UNL     1       3.370   1.308  -1.400  1.00  0.00           C  
HETATM   10  C8  UNL     1       1.961   1.205  -1.435  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.211   1.360  -0.301  1.00  0.00           C  
HETATM   12  N3  UNL     1      -0.178   1.265  -0.300  1.00  0.00           N  
HETATM   13  C10 UNL     1      -1.056   1.011  -1.361  1.00  0.00           C  
HETATM   14  N4  UNL     1      -0.623   0.815  -2.611  1.00  0.00           N  
HETATM   15  C11 UNL     1      -1.477   0.575  -3.605  1.00  0.00           C  
HETATM   16  C12 UNL     1      -2.850   0.529  -3.337  1.00  0.00           C  
HETATM   17  F1  UNL     1      -3.661   0.281  -4.393  1.00  0.00           F  
HETATM   18  C13 UNL     1      -3.316   0.729  -2.055  1.00  0.00           C  
HETATM   19  C14 UNL     1      -4.748   0.675  -1.802  1.00  0.00           C  
HETATM   20  C15 UNL     1      -5.627   1.320  -2.648  1.00  0.00           C  
HETATM   21  C16 UNL     1      -6.988   1.270  -2.411  1.00  0.00           C  
HETATM   22  F2  UNL     1      -7.888   1.900  -3.234  1.00  0.00           F  
HETATM   23  C17 UNL     1      -7.512   0.575  -1.322  1.00  0.00           C  
HETATM   24  N5  UNL     1      -8.768   0.380  -0.882  1.00  0.00           N  
HETATM   25  C18 UNL     1      -8.688  -0.381   0.231  1.00  0.00           C  
HETATM   26  C19 UNL     1      -9.831  -0.864   1.082  1.00  0.00           C  
HETATM   27  N6  UNL     1      -7.391  -0.664   0.493  1.00  0.00           N  
HETATM   28  C20 UNL     1      -6.842  -1.446   1.581  1.00  0.00           C  
HETATM   29  C21 UNL     1      -5.879  -0.639   2.434  1.00  0.00           C  
HETATM   30  C22 UNL     1      -6.235  -2.739   1.111  1.00  0.00           C  
HETATM   31  C23 UNL     1      -6.638  -0.072  -0.472  1.00  0.00           C  
HETATM   32  C24 UNL     1      -5.278  -0.015  -0.719  1.00  0.00           C  
HETATM   33  N7  UNL     1      -2.414   0.965  -1.100  1.00  0.00           N  
HETATM   34  N8  UNL     1       1.889   1.618   0.861  1.00  0.00           N  
HETATM   35  C25 UNL     1       3.220   1.719   0.910  1.00  0.00           C  
HETATM   36  C26 UNL     1       5.689  -0.046   1.481  1.00  0.00           C  
HETATM   37  C27 UNL     1       6.387  -0.967   0.509  1.00  0.00           C  
HETATM   38  H1  UNL     1       9.322  -3.311   1.714  1.00  0.00           H  
HETATM   39  H2  UNL     1       8.043  -3.268   0.476  1.00  0.00           H  
HETATM   40  H3  UNL     1       7.656  -3.051   2.265  1.00  0.00           H  
HETATM   41  H4  UNL     1       9.683  -1.235   0.910  1.00  0.00           H  
HETATM   42  H5  UNL     1       8.562  -0.848   2.293  1.00  0.00           H  
HETATM   43  H6  UNL     1       7.968   1.052  -0.755  1.00  0.00           H  
HETATM   44  H7  UNL     1       9.204   0.778   0.482  1.00  0.00           H  
HETATM   45  H8  UNL     1       7.737   1.315   2.298  1.00  0.00           H  
HETATM   46  H9  UNL     1       7.605   2.594   1.079  1.00  0.00           H  
HETATM   47  H10 UNL     1       5.782   2.730  -0.356  1.00  0.00           H  
HETATM   48  H11 UNL     1       5.936   1.046  -0.914  1.00  0.00           H  
HETATM   49  H12 UNL     1       3.935   1.181  -2.314  1.00  0.00           H  
HETATM   50  H13 UNL     1       1.532   0.998  -2.411  1.00  0.00           H  
HETATM   51  H14 UNL     1      -0.644   1.406   0.658  1.00  0.00           H  
HETATM   52  H15 UNL     1      -1.116   0.416  -4.619  1.00  0.00           H  
HETATM   53  H16 UNL     1      -5.278   1.884  -3.523  1.00  0.00           H  
HETATM   54  H17 UNL     1      -9.768  -1.974   1.212  1.00  0.00           H  
HETATM   55  H18 UNL     1      -9.865  -0.371   2.051  1.00  0.00           H  
HETATM   56  H19 UNL     1     -10.763  -0.696   0.491  1.00  0.00           H  
HETATM   57  H20 UNL     1      -7.699  -1.713   2.247  1.00  0.00           H  
HETATM   58  H21 UNL     1      -5.777   0.406   2.080  1.00  0.00           H  
HETATM   59  H22 UNL     1      -6.200  -0.583   3.495  1.00  0.00           H  
HETATM   60  H23 UNL     1      -4.878  -1.161   2.459  1.00  0.00           H  
HETATM   61  H24 UNL     1      -6.298  -3.459   1.970  1.00  0.00           H  
HETATM   62  H25 UNL     1      -6.867  -3.137   0.298  1.00  0.00           H  
HETATM   63  H26 UNL     1      -5.187  -2.669   0.818  1.00  0.00           H  
HETATM   64  H27 UNL     1      -4.607  -0.514  -0.064  1.00  0.00           H  
HETATM   65  H28 UNL     1       3.721   1.929   1.866  1.00  0.00           H  
HETATM   66  H29 UNL     1       5.987  -0.240   2.524  1.00  0.00           H  
HETATM   67  H30 UNL     1       4.610  -0.236   1.382  1.00  0.00           H  
HETATM   68  H31 UNL     1       5.868  -0.943  -0.468  1.00  0.00           H  
HETATM   69  H32 UNL     1       6.259  -1.997   0.899  1.00  0.00           H  
CONECT    1    2   38   39   40
CONECT    2    3   41   42
CONECT    3    4   37
CONECT    4    5   43   44
CONECT    5    6   45   46
CONECT    6    7   36
CONECT    7    8   47   48
CONECT    8    9    9   35
CONECT    9   10   49
CONECT   10   11   11   50
CONECT   11   12   34
CONECT   12   13   51
CONECT   13   14   14   33
CONECT   14   15
CONECT   15   16   16   52
CONECT   16   17   18
CONECT   18   19   33   33
CONECT   19   20   20   32
CONECT   20   21   53
CONECT   21   22   23   23
CONECT   23   24   31
CONECT   24   25   25
CONECT   25   26   27
CONECT   26   54   55   56
CONECT   27   28   31
CONECT   28   29   30   57
CONECT   29   58   59   60
CONECT   30   61   62   63
CONECT   31   32   32
CONECT   32   64
CONECT   34   35   35
CONECT   35   65
CONECT   36   37   66   67
CONECT   37   68   69
END

HMDB0247749
     RDKit          3D
Abemaciclib
 69 73  0  0  0  0  0  0  0  0999 V2000
    8.3651   -2.8084    1.4473 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6308   -1.3439    1.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7777   -0.6974    0.3393 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1031    0.7013    0.2724 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3814    1.5285    1.2861 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9387    1.3593    1.2023 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4876    1.6932   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0150    1.5691   -0.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3702    1.3085   -1.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9607    1.2051   -1.4346 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2107    1.3599   -0.3011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1777    1.2645   -0.2995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0557    1.0113   -1.3612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6228    0.8146   -2.6114 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4770    0.5752   -3.6053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8504    0.5286   -3.3371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609    0.2809   -4.3929 F   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3160    0.7289   -2.0547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7485    0.6750   -1.8021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6269    1.3198   -2.6484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9875    1.2699   -2.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8884    1.9005   -3.2336 F   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5116    0.5749   -1.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7682    0.3796   -0.8823 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6884   -0.3807    0.2307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8314   -0.8642    1.0818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3913   -0.6640    0.4929 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8418   -1.4458    1.5812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8788   -0.6389    2.4340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2347   -2.7392    1.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6384   -0.0719   -0.4718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2781   -0.0151   -0.7194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4139    0.9645   -1.1002 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8892    1.6183    0.8612 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2198    1.7188    0.9101 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6887   -0.0462    1.4810 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3874   -0.9669    0.5086 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3224   -3.3107    1.7139 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0430   -3.2684    0.4762 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6559   -3.0505    2.2655 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6825   -1.2355    0.9099 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5625   -0.8476    2.2929 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9684    1.0517   -0.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2045    0.7785    0.4816 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7367    1.3151    2.2983 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6050    2.5942    1.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7820    2.7302   -0.3556 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9363    1.0460   -0.9136 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9348    1.1809   -2.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5324    0.9977   -2.4114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6440    1.4062    0.6578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1163    0.4164   -4.6193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2779    1.8835   -3.5226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7681   -1.9744    1.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8653   -0.3706    2.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7632   -0.6958    0.4905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6994   -1.7132    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7767    0.4060    2.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1998   -0.5834    3.4948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8783   -1.1607    2.4590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2982   -3.4585    1.9701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8666   -3.1366    0.2984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1873   -2.6694    0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6074   -0.5135   -0.0642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7207    1.9293    1.8658 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9869   -0.2396    2.5244 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6102   -0.2357    1.3823 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8678   -0.9425   -0.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2587   -1.9969    0.8991 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  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 28 29  1  0
 28 30  1  0
 27 31  1  0
 31 32  2  0
 18 33  2  0
 11 34  1  0
 34 35  2  0
  6 36  1  0
 36 37  1  0
 37  3  1  0
 35  8  1  0
 33 13  1  0
 32 19  1  0
 31 23  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  2 41  1  0
  2 42  1  0
  4 43  1  0
  4 44  1  0
  5 45  1  0
  5 46  1  0
  7 47  1  0
  7 48  1  0
  9 49  1  0
 10 50  1  0
 12 51  1  0
 15 52  1  0
 20 53  1  0
 26 54  1  0
 26 55  1  0
 26 56  1  0
 28 57  1  0
 29 58  1  0
 29 59  1  0
 29 60  1  0
 30 61  1  0
 30 62  1  0
 30 63  1  0
 32 64  1  0
 35 65  1  0
 36 66  1  0
 36 67  1  0
 37 68  1  0
 37 69  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
LY-2835219abemaciclib	ChEMBL
LY2835219	ChEMBL
5-(4-Ethylpiperazin-1-ylmethyl)pyridin-2-yl)-(5-fluoro-4-(7-fluoro-3-isopropyl-2-methyl-3H-benzimidazol-5-yl)pyrimidin-2-yl)amine	MeSH

Chemical Formula

C₂₇H₃₂F₂N₈

Average Molecular Weight

506.606

Monoisotopic Molecular Weight

506.271799388

IUPAC Name

N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzodiazol-6-yl]pyrimidin-2-amine

Traditional Name

N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-(7-fluoro-3-isopropyl-2-methyl-1,3-benzodiazol-5-yl)pyrimidin-2-amine

CAS Registry Number

Not Available

SMILES

CCN1CCN(CC2=CC=C(NC3=NC=C(F)C(=N3)C3=CC(F)=C4N=C(C)N(C(C)C)C4=C3)N=C2)CC1

InChI Identifier

InChI=1S/C27H32F2N8/c1-5-35-8-10-36(11-9-35)16-19-6-7-24(30-14-19)33-27-31-15-22(29)25(34-27)20-12-21(28)26-23(13-20)37(17(2)3)18(4)32-26/h6-7,12-15,17H,5,8-11,16H2,1-4H3,(H,30,31,33,34)

InChI Key

UZWDCWONPYILKI-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
Aminopyridine
Aminopyrimidine
Halopyrimidine
Aralkylamine
N-alkylpiperazine
Aryl fluoride
Aryl halide
1,4-diazinane
N-substituted imidazole
Piperazine
Pyridine
Pyrimidine
Imidolactam
Benzenoid
Imidazole
Azole
Heteroaromatic compound
Tertiary amine
Tertiary aliphatic amine
Azacycle
Organohalogen compound
Organofluoride
Organonitrogen compound
Amine
Organic nitrogen compound
Hydrocarbon derivative
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: HMDB0247749)

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	4.25	ALOGPS
logP	4.42	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	10.27	ChemAxon
pKa (Strongest Basic)	7.94	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	75 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	141.26 m³·mol⁻¹	ChemAxon
Polarizability	54.75 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	220.486	30932474
DeepCCS	[M-H]-	218.091	30932474
DeepCCS	[M-2H]-	250.973	30932474
DeepCCS	[M+Na]+	226.399	30932474
AllCCS	[M+H]+	222.5	32859911
AllCCS	[M+H-H2O]+	220.8	32859911
AllCCS	[M+NH4]+	224.1	32859911
AllCCS	[M+Na]+	224.5	32859911
AllCCS	[M-H]-	214.4	32859911
AllCCS	[M+Na-2H]-	215.6	32859911
AllCCS	[M+HCOO]-	217.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Abemaciclib	CCN1CCN(CC2=CC=C(NC3=NC=C(F)C(=N3)C3=CC(F)=C4N=C(C)N(C(C)C)C4=C3)N=C2)CC1	4729.3	Standard polar	33892256
Abemaciclib	CCN1CCN(CC2=CC=C(NC3=NC=C(F)C(=N3)C3=CC(F)=C4N=C(C)N(C(C)C)C4=C3)N=C2)CC1	3866.0	Standard non polar	33892256
Abemaciclib	CCN1CCN(CC2=CC=C(NC3=NC=C(F)C(=N3)C3=CC(F)=C4N=C(C)N(C(C)C)C4=C3)N=C2)CC1	4260.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Abemaciclib,1TMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C)N=C2)CC1	3944.0	Semi standard non polar	33892256
Abemaciclib,1TMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C)N=C2)CC1	2749.3	Standard non polar	33892256
Abemaciclib,1TMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C)N=C2)CC1	5186.9	Standard polar	33892256
Abemaciclib,1TBDMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C(C)(C)C)N=C2)CC1	4060.3	Semi standard non polar	33892256
Abemaciclib,1TBDMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C(C)(C)C)N=C2)CC1	2967.1	Standard non polar	33892256
Abemaciclib,1TBDMS,isomer #1	CCN1CCN(CC2=CC=C(N(C3=NC=C(F)C(C4=CC(F)=C5N=C(C)N(C(C)C)C5=C4)=N3)[Si](C)(C)C(C)(C)C)N=C2)CC1	5166.5	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 10V, Positive-QTOF	splash10-0a4l-0437290000-1461e4f960ac723bfaf2	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 20V, Positive-QTOF	splash10-0udl-0169200000-e62be43541564b006cc3	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 40V, Positive-QTOF	splash10-0007-1931000000-e7c20a21ab26bef1b7c1	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 10V, Negative-QTOF	splash10-0a4i-0112290000-cdcb0bc7da75c429e9aa	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 20V, Negative-QTOF	splash10-0ik9-0373920000-e74fc8eb3d5eb941a9d0	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 40V, Negative-QTOF	splash10-03dl-9823100000-9812206d50070ff6a282	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 10V, Positive-QTOF	splash10-0a4i-0000090000-ff9afc74b9c13694a028	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 20V, Positive-QTOF	splash10-0a4i-0003390000-4688a552a4bd5ea41604	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 40V, Positive-QTOF	splash10-0f6w-0009600000-5e0fb640aab0112f458c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 10V, Negative-QTOF	splash10-0a4i-0000290000-4bfbe64c105bcd975721	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 20V, Negative-QTOF	splash10-0a4i-0000980000-fc29c877204a1115f83f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Abemaciclib 40V, Negative-QTOF	splash10-001l-0054910000-508fc07ce9878a69b360	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

DB12001

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

29340700

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Abemaciclib

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 Abemaciclib (HMDB0247749)

MOL for HMDB0247749 (Abemaciclib)

3D MOL for HMDB0247749 (Abemaciclib)

3D SDF for HMDB0247749 (Abemaciclib)

3D-SDF for HMDB0247749 (Abemaciclib)

PDB for HMDB0247749 (Abemaciclib)

3D PDB for HMDB0247749 (Abemaciclib)

SMILES for HMDB0247749 (Abemaciclib)

INCHI for HMDB0247749 (Abemaciclib)

Structure for HMDB0247749 (Abemaciclib)

3D Structure for HMDB0247749 (Abemaciclib)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

MS/MS Spectra