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Showing metabocard for Clonidine (HMDB0014714)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:43 UTC
HMDB IDHMDB0014714
Secondary Accession Numbers
  • HMDB14714
Metabolite Identification
Common NameClonidine
DescriptionClonidine, an imidazoline-derivative hypotensive agent is a centrally-acting α2-adrenergic agonist. It crosses the blood-brain barrier and acts in the hypothalamus to induce a decrease in blood pressure. It may also be administered as an epidural infusion as an adjunct treatment in the management of severe cancer pain that is not relieved by opiate analgesics alone. Clonidine may be used for differential diagnosis of pheochromocytoma in hypertensive patients. Other uses for clonidine include prophylaxis of vascular migraine headaches, treatment of severe dysmenorrhea, management of vasomotor symptoms associated with menopause, rapid detoxification in the management of opiate withdrawal, treatment of alcohol withdrawal used in conjunction with benzodiazepines, management of nicotine dependence, topical use to reduce intraocular pressure in the treatment of open-angle and secondary glaucoma and hemorrhagic glaucoma associated with hypertension, and in the treatment of attention-deficit hyperactivity disorder (ADHD). Clonidine also exhibits some peripheral activity.
Structure
Data?1582753212
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0014714 (Clonidine)

575
  Mrv0541 02231214472D          

 14 15  0  0  0  0            999 V2000
    4.5080   -0.3751    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.3751    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.8797    1.6829    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5472    0.5269    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6868    1.8544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0993    1.1399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.3751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.7876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.7876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -1.6127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.6127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -2.0252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3  6  1  0  0  0  0
  3  8  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  2  0  0  0  0
  6  7  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  2  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
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3D MOL for HMDB0014714 (Clonidine)

HMDB0014714
     RDKit          3D
Clonidine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.3961   -2.5034    1.5118 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.4226   -1.0291    0.5391 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6384   -0.4846    0.1783 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6795    0.6622   -0.5784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4738    1.2161   -0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2435    0.6646   -0.5770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2498    1.4271   -1.0781 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.2043   -0.4776    0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0034   -1.0928    0.5841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2885   -0.5968    0.2585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0106   -0.9821   -0.7339 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2758   -0.2744   -0.7860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3170    0.6020    0.4360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9855    0.4088    0.9849 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5689   -0.9581    0.4896 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6343    1.0913   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4880    2.1141   -1.5349 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0542   -1.9809    1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0844   -1.0523   -0.7834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3774    0.3664   -1.6676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0332    0.2441    1.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270    1.6631    0.2140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6509    0.9722    1.8086 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
  8  2  1  0
 14 10  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  9 18  1  0
 12 19  1  0
 12 20  1  0
 13 21  1  0
 13 22  1  0
 14 23  1  0
M  END
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3D SDF for HMDB0014714 (Clonidine)

575
  Mrv0541 02231214472D          

 14 15  0  0  0  0            999 V2000
    4.5080   -0.3751    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.3751    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.8797    1.6829    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5472    0.5269    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6868    1.8544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0993    1.1399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.8624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.3751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.7876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.7876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -1.6127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.6127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -2.0252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3  6  1  0  0  0  0
  3  8  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  2  0  0  0  0
  6  7  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  2  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014714

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=CC=CC(Cl)=C1NC1=NCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C9H9Cl2N3/c10-6-2-1-3-7(11)8(6)14-9-12-4-5-13-9/h1-3H,4-5H2,(H2,12,13,14)

> <INCHI_KEY>
GJSURZIOUXUGAL-UHFFFAOYSA-N

> <FORMULA>
C9H9Cl2N3

> <MOLECULAR_WEIGHT>
230.094

> <EXACT_MASS>
229.017352717

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
21.69630745656319

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-(2,6-dichlorophenyl)-4,5-dihydro-1H-imidazol-2-amine

> <ALOGPS_LOGP>
2.55

> <JCHEM_LOGP>
2.4850887036666673

> <ALOGPS_LOGS>
-2.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.164017075161533

> <JCHEM_POLAR_SURFACE_AREA>
36.42

> <JCHEM_REFRACTIVITY>
59.088800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.80e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
clonidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0014714 (Clonidine)

HMDB0014714
     RDKit          3D
Clonidine
 23 24  0  0  0  0  0  0  0  0999 V2000
    2.3961   -2.5034    1.5118 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.4226   -1.0291    0.5391 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6384   -0.4846    0.1783 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6795    0.6622   -0.5784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4738    1.2161   -0.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2435    0.6646   -0.5770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2498    1.4271   -1.0781 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.2043   -0.4776    0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0034   -1.0928    0.5841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2885   -0.5968    0.2585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0106   -0.9821   -0.7339 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2758   -0.2744   -0.7860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3170    0.6020    0.4360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9855    0.4088    0.9849 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5689   -0.9581    0.4896 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6343    1.0913   -0.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4880    2.1141   -1.5349 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0542   -1.9809    1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0844   -1.0523   -0.7834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3774    0.3664   -1.6676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0332    0.2441    1.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5270    1.6631    0.2140 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6509    0.9722    1.8086 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
  8  2  1  0
 14 10  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  9 18  1  0
 12 19  1  0
 12 20  1  0
 13 21  1  0
 13 22  1  0
 14 23  1  0
M  END
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PDB for HMDB0014714 (Clonidine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 575                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Cl   UNK     0       8.415  -0.700   0.000  0.00  0.00          Cl+0
HETATM    2 Cl   UNK     0       3.080  -0.700   0.000  0.00  0.00          Cl+0
HETATM    3  N   UNK     0       7.242   3.141   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       5.748   0.840   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       8.488   0.984   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       8.749   3.462   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.519   2.128   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.081   1.610   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.748  -0.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.081  -1.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.414  -1.470   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081  -3.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.414  -3.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.748  -3.780   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3    6    8                                                       
CONECT    4    8    9                                                       
CONECT    5    7    8                                                       
CONECT    6    3    7                                                       
CONECT    7    5    6                                                       
CONECT    8    3    4    5                                                  
CONECT    9    4   10   11                                                  
CONECT   10    1    9   12                                                  
CONECT   11    2    9   13                                                  
CONECT   12   10   14                                                       
CONECT   13   11   14                                                       
CONECT   14   12   13                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0014714 (Clonidine)

COMPND    HMDB0014714
HETATM    1 CL1  UNL     1       2.396  -2.503   1.512  1.00  0.00          CL  
HETATM    2  C1  UNL     1       2.423  -1.029   0.539  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.638  -0.485   0.178  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.679   0.662  -0.578  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.474   1.216  -0.942  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.243   0.665  -0.577  1.00  0.00           C  
HETATM    7 CL2  UNL     1      -0.250   1.427  -1.078  1.00  0.00          CL  
HETATM    8  C6  UNL     1       1.204  -0.478   0.177  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.003  -1.093   0.584  1.00  0.00           N  
HETATM   10  C7  UNL     1      -1.288  -0.597   0.259  1.00  0.00           C  
HETATM   11  N2  UNL     1      -2.011  -0.982  -0.734  1.00  0.00           N  
HETATM   12  C8  UNL     1      -3.276  -0.274  -0.786  1.00  0.00           C  
HETATM   13  C9  UNL     1      -3.317   0.602   0.436  1.00  0.00           C  
HETATM   14  N3  UNL     1      -1.986   0.409   0.985  1.00  0.00           N  
HETATM   15  H1  UNL     1       4.569  -0.958   0.490  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.634   1.091  -0.863  1.00  0.00           H  
HETATM   17  H3  UNL     1       2.488   2.114  -1.535  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.054  -1.981   1.170  1.00  0.00           H  
HETATM   19  H5  UNL     1      -4.084  -1.052  -0.783  1.00  0.00           H  
HETATM   20  H6  UNL     1      -3.377   0.366  -1.668  1.00  0.00           H  
HETATM   21  H7  UNL     1      -4.033   0.244   1.193  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.527   1.663   0.214  1.00  0.00           H  
HETATM   23  H9  UNL     1      -1.651   0.972   1.809  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3    8
CONECT    3    4   15
CONECT    4    5    5   16
CONECT    5    6   17
CONECT    6    7    8    8
CONECT    8    9
CONECT    9   10   18
CONECT   10   11   11   14
CONECT   11   12
CONECT   12   13   19   20
CONECT   13   14   21   22
CONECT   14   23
END
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SMILES for HMDB0014714 (Clonidine)

ClC1=CC=CC(Cl)=C1NC1=NCCN1
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INCHI for HMDB0014714 (Clonidine)

InChI=1S/C9H9Cl2N3/c10-6-2-1-3-7(11)8(6)14-9-12-4-5-13-9/h1-3H,4-5H2,(H2,12,13,14)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC9H9Cl2N3
Average Molecular Weight230.094
Monoisotopic Molecular Weight229.017352717
IUPAC NameN-(2,6-dichlorophenyl)-4,5-dihydro-1H-imidazol-2-amine
Traditional Nameclonidine
CAS Registry Number4205-90-7
SMILES
ClC1=CC=CC(Cl)=C1NC1=NCCN1
InChI Identifier
InChI=1S/C9H9Cl2N3/c10-6-2-1-3-7(11)8(6)14-9-12-4-5-13-9/h1-3H,4-5H2,(H2,12,13,14)
InChI KeyGJSURZIOUXUGAL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dichlorobenzenes. Dichlorobenzenes are compounds containing a benzene with exactly two chlorine atoms attached to it.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassHalobenzenes
Direct ParentDichlorobenzenes
Alternative Parents
Substituents
  • 1,3-dichlorobenzene
  • Aniline or substituted anilines
  • Aryl chloride
  • Aryl halide
  • 2-imidazoline
  • Guanidine
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point130 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.48 g/LNot Available
LogP2.7Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+CBM144.030932474
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00575 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00575 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00575
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2701
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClonidine
METLIN IDNot Available
PubChem Compound2803
PDB IDCLU
ChEBI ID3757
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hossmann V, Maling TJ, Hamilton CA, Reid JL, Dollery CT: Sedative and cardiovascular effects of clonidine and nitrazepam. Clin Pharmacol Ther. 1980 Aug;28(2):167-76. [PubMed:7398184 ]
  2. Schapiro NA: "Dude, you don't have Tourette's:" Tourette's syndrome, beyond the tics. Pediatr Nurs. 2002 May-Jun;28(3):243-6, 249-53. [PubMed:12087644 ]