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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:50 UTC

Update Date

2023-02-21 17:18:17 UTC

HMDB ID

HMDB0014771

Secondary Accession Numbers

HMDB14771

Metabolite Identification

Common Name

Dexmedetomidine

Description

Dexmedetomidine is only found in individuals that have used or taken this drug. It is an agonist of receptors, adrenergic alpha-2 that is used in veterinary medicine for its analgesic and sedative properties. It is the racemate of dexmedetomidine. [PubChem]Dexmedetomidine is a specific and selective alpha-2 adrenoceptor agonist. By binding to the presynaptic alpha-2 adrenoceptors, it inhibits the release if norepinephrine, therefore, terminate the propagation of pain signals. Activation of the postsynaptic alpha-2 adrenoceptors inhibits the sympathetic activity decreases blood pressure and heart rate.

Structure

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

HMDB0014771
     RDKit          3D
Dexmedetomidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    3.6636   -0.0857    0.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3773    0.4997    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2294    1.8703    0.4333 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207    2.3679    0.0082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0176    1.5092   -0.3970 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1895    0.1313   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9361   -0.6902   -0.8385 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1717   -0.5350   -2.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459   -0.2495   -0.0791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -0.7467    1.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6358   -0.1459    1.5539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9708    0.7141    0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0675    0.6619   -0.4300 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3834   -0.3659    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6150   -1.8086    0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1047   -0.7316    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4207    0.7240    1.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5513   -0.6393    1.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0247    2.5106    0.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981    3.4488    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9041    1.9838   -0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8352   -1.7648   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1526   -0.6758   -2.8008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7921   -1.3668   -2.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5347    0.4601   -2.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9791   -1.5081    1.7419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1593   -0.3168    2.4597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8512    1.3589    0.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -2.0113    0.7788 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7661   -2.4053    0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9276   -2.1932   -0.9369 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
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
  6 14  2  0
 14 15  1  0
 14  2  1  0
 13  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  7 22  1  6
  8 23  1  0
  8 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
 15 30  1  0
 15 31  1  0
M  END


  Mrv0541 04191212132D          

 15 16  0  0  1  0            999 V2000
    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9840    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  2  0  0  0  0
  2  1  1  0  0  0  0
  2  8  2  0  0  0  0
  3 12  2  0  0  0  0
  4  3  1  0  0  0  0
  4  2  1  0  0  0  0
  4  6  1  1  0  0  0
  3  5  1  0  0  0  0
  5  7  2  0  0  0  0
 12 14  1  0  0  0  0
  7  9  1  0  0  0  0
 14  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 13  1  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014771

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H](C1=CNC=N1)C1=C(C)C(C)=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H16N2/c1-9-5-4-6-12(10(9)2)11(3)13-7-14-8-15-13/h4-8,11H,1-3H3,(H,14,15)/t11-/m0/s1

> <INCHI_KEY>
CUHVIMMYOGQXCV-NSHDSACASA-N

> <FORMULA>
C13H16N2

> <MOLECULAR_WEIGHT>
200.2795

> <EXACT_MASS>
200.131348522

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
23.316122776005628

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-[(1S)-1-(2,3-dimethylphenyl)ethyl]-1H-imidazole

> <ALOGPS_LOGP>
3.28

> <JCHEM_LOGP>
3.390314838666667

> <ALOGPS_LOGS>
-3.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.088405723755134

> <JCHEM_PKA_STRONGEST_BASIC>
6.544347475468593

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
62.9831

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dexmedetomidine hcl

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0014771
     RDKit          3D
Dexmedetomidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    3.6636   -0.0857    0.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3773    0.4997    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2294    1.8703    0.4333 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207    2.3679    0.0082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0176    1.5092   -0.3970 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1895    0.1313   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9361   -0.6902   -0.8385 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1717   -0.5350   -2.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459   -0.2495   -0.0791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -0.7467    1.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6358   -0.1459    1.5539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9708    0.7141    0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0675    0.6619   -0.4300 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3834   -0.3659    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6150   -1.8086    0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1047   -0.7316    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4207    0.7240    1.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5513   -0.6393    1.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0247    2.5106    0.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981    3.4488    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9041    1.9838   -0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8352   -1.7648   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1526   -0.6758   -2.8008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7921   -1.3668   -2.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5347    0.4601   -2.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9791   -1.5081    1.7419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1593   -0.3168    2.4597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8512    1.3589    0.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -2.0113    0.7788 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7661   -2.4053    0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9276   -2.1932   -0.9369 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
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
  6 14  2  0
 14 15  1  0
 14  2  1  0
 13  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  7 22  1  6
  8 23  1  0
  8 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
 15 30  1  0
 15 31  1  0
M  END

HEADER    PROTEIN                                 19-APR-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-12         0                                  
HETATM    1  N   UNK     0       1.334   0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.798  -1.246   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001   0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       3.703   0.000   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.798   1.246   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335  -1.540   0.000  0.00  0.00           C+0
CONECT    1   11    2                                                       
CONECT    2    1    8    4                                                  
CONECT    3   12    4    5                                                  
CONECT    4    3    2    6                                                  
CONECT    5    3    7                                                       
CONECT    6    4                                                            
CONECT    7    5    9                                                       
CONECT    8    2   10                                                       
CONECT    9    7   14                                                       
CONECT   10    8   11                                                       
CONECT   11    1   10                                                       
CONECT   12    3   14   13                                                  
CONECT   13   12                                                            
CONECT   14   12    9   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0014771
HETATM    1  C1  UNL     1       3.664  -0.086   0.882  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.377   0.500   0.431  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.229   1.870   0.433  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.021   2.368   0.008  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.018   1.509  -0.397  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.190   0.131  -0.391  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.936  -0.690  -0.839  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.172  -0.535  -2.341  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.146  -0.249  -0.079  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.505  -0.747   1.153  1.00  0.00           C  
HETATM   11  N1  UNL     1      -3.636  -0.146   1.554  1.00  0.00           N  
HETATM   12  C11 UNL     1      -3.971   0.714   0.577  1.00  0.00           C  
HETATM   13  N2  UNL     1      -3.067   0.662  -0.430  1.00  0.00           N  
HETATM   14  C12 UNL     1       1.383  -0.366   0.029  1.00  0.00           C  
HETATM   15  C13 UNL     1       1.615  -1.809   0.056  1.00  0.00           C  
HETATM   16  H1  UNL     1       4.105  -0.732   0.086  1.00  0.00           H  
HETATM   17  H2  UNL     1       4.421   0.724   1.057  1.00  0.00           H  
HETATM   18  H3  UNL     1       3.551  -0.639   1.831  1.00  0.00           H  
HETATM   19  H4  UNL     1       3.025   2.511   0.751  1.00  0.00           H  
HETATM   20  H5  UNL     1       0.898   3.449   0.007  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.904   1.984  -0.716  1.00  0.00           H  
HETATM   22  H7  UNL     1      -0.835  -1.765  -0.657  1.00  0.00           H  
HETATM   23  H8  UNL     1      -0.153  -0.676  -2.801  1.00  0.00           H  
HETATM   24  H9  UNL     1      -1.792  -1.367  -2.682  1.00  0.00           H  
HETATM   25  H10 UNL     1      -1.535   0.460  -2.599  1.00  0.00           H  
HETATM   26  H11 UNL     1      -1.979  -1.508   1.742  1.00  0.00           H  
HETATM   27  H12 UNL     1      -4.159  -0.317   2.460  1.00  0.00           H  
HETATM   28  H13 UNL     1      -4.851   1.359   0.602  1.00  0.00           H  
HETATM   29  H14 UNL     1       2.451  -2.011   0.779  1.00  0.00           H  
HETATM   30  H15 UNL     1       0.766  -2.405   0.431  1.00  0.00           H  
HETATM   31  H16 UNL     1       1.928  -2.193  -0.937  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3   14
CONECT    3    4   19
CONECT    4    5    5   20
CONECT    5    6   21
CONECT    6    7   14   14
CONECT    7    8    9   22
CONECT    8   23   24   25
CONECT    9   10   10   13
CONECT   10   11   26
CONECT   11   12   27
CONECT   12   13   13   28
CONECT   14   15
CONECT   15   29   30   31
END

HMDB0014771
     RDKit          3D
Dexmedetomidine
 31 32  0  0  0  0  0  0  0  0999 V2000
    3.6636   -0.0857    0.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3773    0.4997    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2294    1.8703    0.4333 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0207    2.3679    0.0082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0176    1.5092   -0.3970 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1895    0.1313   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9361   -0.6902   -0.8385 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1717   -0.5350   -2.3410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1459   -0.2495   -0.0791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -0.7467    1.1530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6358   -0.1459    1.5539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9708    0.7141    0.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0675    0.6619   -0.4300 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3834   -0.3659    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6150   -1.8086    0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1047   -0.7316    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4207    0.7240    1.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5513   -0.6393    1.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0247    2.5106    0.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981    3.4488    0.0070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9041    1.9838   -0.7165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8352   -1.7648   -0.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1526   -0.6758   -2.8008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7921   -1.3668   -2.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5347    0.4601   -2.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9791   -1.5081    1.7419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1593   -0.3168    2.4597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8512    1.3589    0.6023 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4509   -2.0113    0.7788 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7661   -2.4053    0.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9276   -2.1932   -0.9369 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
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
  6 14  2  0
 14 15  1  0
 14  2  1  0
 13  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  7 22  1  6
  8 23  1  0
  8 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
 15 30  1  0
 15 31  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(+)-4-((S)-alpha,2,3-Trimethylbenzyl)imidazole	ChEBI
Dexmedetomidina	ChEBI
Dexmedetomidinum	ChEBI
MPV 1440	ChEBI
Dexdor	Kegg
Precedex	Kegg
(+)-4-((S)-a,2,3-Trimethylbenzyl)imidazole	Generator
(+)-4-((S)-Α,2,3-trimethylbenzyl)imidazole	Generator
Medetomidine	HMDB
Hospira brand OF dexmedetomidine hydrochloride	HMDB
Hydrochloride, dexmedetomidine	HMDB
Dexmedetomidine hydrochloride	HMDB

Chemical Formula

C₁₃H₁₆N₂

Average Molecular Weight

200.2795

Monoisotopic Molecular Weight

200.131348522

IUPAC Name

4-[(1S)-1-(2,3-dimethylphenyl)ethyl]-1H-imidazole

Traditional Name

dexmedetomidine hcl

CAS Registry Number

113775-47-6

SMILES

C[C@H](C1=CNC=N1)C1=C(C)C(C)=CC=C1

InChI Identifier

InChI=1S/C13H16N2/c1-9-5-4-6-12(10(9)2)11(3)13-7-14-8-15-13/h4-8,11H,1-3H3,(H,14,15)/t11-/m0/s1

InChI Key

CUHVIMMYOGQXCV-NSHDSACASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-xylenes. These are aromatic compounds that contain a o-xylene moiety, which is a monocyclic benzene carrying exactly two methyl groups at the 1- and 2-positions.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Xylenes

Direct Parent

o-Xylenes

Alternative Parents

Substituents

O-xylene
Heteroaromatic compound
Imidazole
Azole
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

medetomidine (CHEBI:4466 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Membrane (HMDB: HMDB0014771)

Source

Exogenous

Exogenous (HMDB: HMDB0014771)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.17 g/L	Not Available
LogP	2.8	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.17 g/L	ALOGPS
logP	3.28	ALOGPS
logP	3.39	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	14.09	ChemAxon
pKa (Strongest Basic)	6.54	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	28.68 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.98 m³·mol⁻¹	ChemAxon
Polarizability	23.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	147.079	31661259
DarkChem	[M-H]-	148.976	31661259
DeepCCS	[M+H]+	152.212	30932474
DeepCCS	[M-H]-	149.816	30932474
DeepCCS	[M-2H]-	182.852	30932474
DeepCCS	[M+Na]+	158.203	30932474
AllCCS	[M+H]+	142.8	32859911
AllCCS	[M+H-H2O]+	138.4	32859911
AllCCS	[M+NH4]+	146.9	32859911
AllCCS	[M+Na]+	148.1	32859911
AllCCS	[M-H]-	150.2	32859911
AllCCS	[M+Na-2H]-	150.4	32859911
AllCCS	[M+HCOO]-	150.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	5.6 minutes	32390414
Predicted by Siyang on May 30, 2022	11.1968 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.48 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	26.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1255.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	303.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	143.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	180.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	96.2 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	484.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	435.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	65.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	940.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	379.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1200.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	303.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	299.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	288.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	161.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	20.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dexmedetomidine	C[C@H](C1=CNC=N1)C1=C(C)C(C)=CC=C1	2548.1	Standard polar	33892256
Dexmedetomidine	C[C@H](C1=CNC=N1)C1=C(C)C(C)=CC=C1	1822.6	Standard non polar	33892256
Dexmedetomidine	C[C@H](C1=CNC=N1)C1=C(C)C(C)=CC=C1	1934.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Dexmedetomidine,1TMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C)C=N2)=C1C	1942.2	Semi standard non polar	33892256
Dexmedetomidine,1TMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C)C=N2)=C1C	1931.0	Standard non polar	33892256
Dexmedetomidine,1TMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C)C=N2)=C1C	2221.1	Standard polar	33892256
Dexmedetomidine,1TBDMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C(C)(C)C)C=N2)=C1C	2175.4	Semi standard non polar	33892256
Dexmedetomidine,1TBDMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C(C)(C)C)C=N2)=C1C	2091.2	Standard non polar	33892256
Dexmedetomidine,1TBDMS,isomer #1	CC1=CC=CC([C@H](C)C2=CN([Si](C)(C)C(C)(C)C)C=N2)=C1C	2339.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dexmedetomidine GC-MS (Non-derivatized) - 70eV, Positive	splash10-001r-3900000000-1af3ca78fb22ea06ac9d	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dexmedetomidine 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 - Dexmedetomidine 10V, Positive-QTOF	splash10-0udi-0290000000-a37775586d59da8a5c1d	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 20V, Positive-QTOF	splash10-0uk9-1950000000-1f473c29f9a4392cf069	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 40V, Positive-QTOF	splash10-0a4i-1900000000-05caba97ecbe584d9c19	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 10V, Negative-QTOF	splash10-0002-0900000000-b4978ed90cadc637e3fb	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 20V, Negative-QTOF	splash10-0002-1900000000-b7da7a8cb234743e8c21	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 40V, Negative-QTOF	splash10-0awc-4900000000-2ac7ce450e11fc5753d7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 10V, Positive-QTOF	splash10-0udi-1290000000-7ce023520ec9d746eea7	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 20V, Positive-QTOF	splash10-0002-7910000000-4ae55943a38333ee5287	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 40V, Positive-QTOF	splash10-0gdl-9800000000-cd3153463e2e91d489be	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 10V, Negative-QTOF	splash10-0002-1900000000-03c59d592e0c63c3b129	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 20V, Negative-QTOF	splash10-05r0-4900000000-63211e5f1011b3b9b21b	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dexmedetomidine 40V, Negative-QTOF	splash10-0690-4900000000-aa17f9adf1fe8fc096d3	2021-10-11	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00633	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00633	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00633

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4470605

KEGG Compound ID

C07450

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dexmedetomidine

METLIN ID

Not Available

PubChem Compound

5311068

PDB ID

Not Available

ChEBI ID

4466

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

Enzymes

Enzyme Details

1. Cytochrome P450 2E1

General function:: Involved in monooxygenase activity
Specific function:: Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.
Gene Name:: CYP2E1
Uniprot ID:: P05181
Molecular weight:: 56848.42

References

Avsaroglu H, Bull S, Maas-Bakker RF, Scherpenisse P, Van Lith HA, Bergwerff AA, Hellebrekers LJ, Van Zutphen LF, Fink-Gremmels J: Differences in hepatic cytochrome P450 activity correlate with the strain-specific biotransformation of medetomidine in AX/JU and IIIVO/JU inbred rabbits. J Vet Pharmacol Ther. 2008 Aug;31(4):368-77. doi: 10.1111/j.1365-2885.2008.00969.x. [PubMed:18638298 ]
Duhamel MC, Troncy E, Beaudry F: Metabolic stability and determination of cytochrome P450 isoenzymes' contribution to the metabolism of medetomidine in dog liver microsomes. Biomed Chromatogr. 2010 Aug;24(8):868-77. doi: 10.1002/bmc.1379. [PubMed:20020418 ]

Enzyme Details

2. Cytochrome P450 2D6

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.
Gene Name:: CYP2D6
Uniprot ID:: P10635
Molecular weight:: 55768.94

References

Rodrigues AD, Roberts EM: The in vitro interaction of dexmedetomidine with human liver microsomal cytochrome P4502D6 (CYP2D6). Drug Metab Dispos. 1997 May;25(5):651-5. [PubMed:9152607 ]

Enzyme Details

3. Cytochrome P450 1A1

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
Gene Name:: CYP1A1
Uniprot ID:: P04798
Molecular weight:: 58164.815

References

Konstandi M, Kostakis D, Harkitis P, Marselos M, Johnson EO, Adamidis K, Lang MA: Role of adrenoceptor-linked signaling pathways in the regulation of CYP1A1 gene expression. Biochem Pharmacol. 2005 Jan 15;69(2):277-87. [PubMed:15627480 ]

Enzyme Details

4. Cytochrome P450 1A2

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:: CYP1A2
Uniprot ID:: P05177
Molecular weight:: 58406.915

References

Konstandi M, Lang MA, Kostakis D, Johnson EO, Marselos M: Predominant role of peripheral catecholamines in the stress-induced modulation of CYP1A2 inducibility by benzo(alpha)pyrene. Basic Clin Pharmacol Toxicol. 2008 Jan;102(1):35-44. Epub 2007 Oct 31. [PubMed:17973897 ]
Konstandi M, Kostakis D, Harkitis P, Johnson EO, Marselos M, Adamidis K, Lang MA: Benzo(alpha)pyrene-induced up-regulation of CYP1A2 gene expression: role of adrenoceptor-linked signaling pathways. Life Sci. 2006 Jun 20;79(4):331-41. Epub 2006 Feb 28. [PubMed:16510159 ]

Enzyme Details

5. Alpha-2A adrenergic receptor

General function:: Involved in G-protein coupled receptor protein signaling pathway
Specific function:: Alpha-2 adrenergic receptors mediate the catecholamine- induced inhibition of adenylate cyclase through the action of G proteins. The rank order of potency for agonists of this receptor is oxymetazoline > clonidine > epinephrine > norepinephrine > phenylephrine > dopamine > p-synephrine > p-tyramine > serotonin = p-octopamine. For antagonists, the rank order is yohimbine > phentolamine = mianserine > chlorpromazine = spiperone = prazosin > propanolol > alprenolol = pindolol
Gene Name:: ADRA2A
Uniprot ID:: P08913
Molecular weight:: 48956.3

References

Fairbanks CA, Stone LS, Kitto KF, Nguyen HO, Posthumus IJ, Wilcox GL: alpha(2C)-Adrenergic receptors mediate spinal analgesia and adrenergic-opioid synergy. J Pharmacol Exp Ther. 2002 Jan;300(1):282-90. [PubMed:11752127 ]
Scheibner J, Trendelenburg AU, Hein L, Starke K, Blandizzi C: Alpha 2-adrenoceptors in the enteric nervous system: a study in alpha 2A-adrenoceptor-deficient mice. Br J Pharmacol. 2002 Feb;135(3):697-704. [PubMed:11834617 ]
Davies MF, Tsui J, Flannery JA, Li X, DeLorey TM, Hoffman BB: Activation of alpha2 adrenergic receptors suppresses fear conditioning: expression of c-Fos and phosphorylated CREB in mouse amygdala. Neuropsychopharmacology. 2004 Feb;29(2):229-39. [PubMed:14583739 ]
Dawson C, Ma D, Chow A, Maze M: Dexmedetomidine enhances analgesic action of nitrous oxide: mechanisms of action. Anesthesiology. 2004 Apr;100(4):894-904. [PubMed:15087625 ]
Ozdogan UK, Lahdesmaki J, Hakala K, Scheinin M: The involvement of alpha 2A-adrenoceptors in morphine analgesia, tolerance and withdrawal in mice. Eur J Pharmacol. 2004 Aug 23;497(2):161-71. [PubMed:15306201 ]
Menon DV, Wang Z, Fadel PJ, Arbique D, Leonard D, Li JL, Victor RG, Vongpatanasin W: Central sympatholysis as a novel countermeasure for cocaine-induced sympathetic activation and vasoconstriction in humans. J Am Coll Cardiol. 2007 Aug 14;50(7):626-33. Epub 2007 Jul 30. [PubMed:17692748 ]

Showing metabocard for Dexmedetomidine (HMDB0014771)

MOL for HMDB0014771 (Dexmedetomidine)

3D MOL for HMDB0014771 (Dexmedetomidine)

3D SDF for HMDB0014771 (Dexmedetomidine)

3D-SDF for HMDB0014771 (Dexmedetomidine)

PDB for HMDB0014771 (Dexmedetomidine)

3D PDB for HMDB0014771 (Dexmedetomidine)

SMILES for HMDB0014771 (Dexmedetomidine)

INCHI for HMDB0014771 (Dexmedetomidine)

Structure for HMDB0014771 (Dexmedetomidine)

3D Structure for HMDB0014771 (Dexmedetomidine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra

Enzymes

References

References

References

References

References