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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-04 18:58:47 UTC

Update Date

2019-07-23 07:15:04 UTC

HMDB ID

HMDB0060777

Secondary Accession Numbers

HMDB60777

Metabolite Identification

Common Name

5-Hydroxyemedastine

Description

5-Hydroxyemedastine belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). 5-Hydroxyemedastine is a very strong basic compound (based on its pKa). It's mechanism of action is a H1 receptor antagonist. Emedastine difumarate (Emadine) is a second generation antihistamine used in eye drops to treat allergic conjunctivitis. 5-Hydroxyemedastine is a metabolite of emedastine.

Structure

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

HMDB0060777
     RDKit          3D
5-Hydroxyemedastine
 49 51  0  0  0  0  0  0  0  0999 V2000
    3.2366    3.4669   -0.4548 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8901    2.7494    0.7316 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9680    1.9194    1.3657 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4895    0.9677    0.4879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4763    0.0663    1.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9488   -0.9388    0.3398 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1532   -0.8608   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1047    0.1507   -0.5489 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0803    1.3584    0.1905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1414    2.3580   -0.3150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5186    1.9279    0.1208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1131    0.9766   -0.7702 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5193    0.8461   -0.4755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4370   -0.3051   -0.7471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1616   -0.1433   -1.5479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2537   -2.0436   -1.0939 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7588   -2.8501   -0.7821 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1454   -4.1267   -1.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2814   -4.7089   -0.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6797   -5.9988   -1.0249 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -3.9755    0.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6843   -2.7191    0.6699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5221   -2.1603    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1528    3.6062   -0.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7714    4.3978   -0.6514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3241    2.7630   -1.3155 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3141    3.4714    1.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7239    2.1323    0.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1139    1.3476   -0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3531    0.2960    0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364   -0.4696    1.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7820    0.6066    1.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1535    1.9062    0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4206    1.2055    1.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0451    2.5504   -1.3824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9159    3.3119    0.2191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1616    2.8297    0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.5517    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9974    1.8122   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9621   -0.0269   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6541    0.8173    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2538   -0.6701    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1372   -1.0278   -1.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9578   -1.0801   -2.0764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2202    0.7139   -2.2580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5139   -4.6312   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3721   -6.8216   -0.5299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9125   -4.4208    0.6754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2356   -2.1280    1.3713 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  7 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 23  6  1  0
 15  8  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 14 43  1  0
 15 44  1  0
 15 45  1  0
 18 46  1  0
 20 47  1  0
 21 48  1  0
 22 49  1  0
M  END


  Mrv0541 07041311582D          

 23 25  0  0  0  0            999 V2000
    0.7425   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5239   -5.5020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4569   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5750   -4.4969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1040    0.1934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8490   -0.5912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2123   -5.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5874   -3.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3883   -4.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0415   -3.3629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6004   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8859   -2.0248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4630   -0.2481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9109    0.3649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2080   -1.0328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4011   -1.2043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0685   -2.3603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6205   -1.7472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0193   -4.8493    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2400   -3.1673    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3148   -2.0248    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1659    1.1496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1714   -2.4373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  1  0  0  0  0
  8  4  1  0  0  0  0
 10  9  1  0  0  0  0
 12 11  1  0  0  0  0
 14  5  1  0  0  0  0
 14 13  2  0  0  0  0
 15 13  1  0  0  0  0
 16  6  1  0  0  0  0
 16 15  2  0  0  0  0
 18 15  1  0  0  0  0
 18 17  2  0  0  0  0
 19  2  1  0  0  0  0
 19  7  1  0  0  0  0
 19  9  1  0  0  0  0
 20  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 17  1  0  0  0  0
 21 11  1  0  0  0  0
 21 16  1  0  0  0  0
 21 17  1  0  0  0  0
 22 14  1  0  0  0  0
 23  3  1  0  0  0  0
 23 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060777

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOCCN1C(=NC2=C1C=CC(O)=C2)N1CCCN(C)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C17H26N4O2/c1-3-23-12-11-21-16-6-5-14(22)13-15(16)18-17(21)20-8-4-7-19(2)9-10-20/h5-6,13,22H,3-4,7-12H2,1-2H3

> <INCHI_KEY>
JNLXTCQXMDMAOC-UHFFFAOYSA-N

> <FORMULA>
C17H26N4O2

> <MOLECULAR_WEIGHT>
318.4139

> <EXACT_MASS>
318.205576096

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
36.595230522969494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(2-ethoxyethyl)-2-(4-methyl-1,4-diazepan-1-yl)-1H-1,3-benzodiazol-5-ol

> <ALOGPS_LOGP>
2.42

> <JCHEM_LOGP>
1.778538399659138

> <ALOGPS_LOGS>
-2.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.260390242652077

> <JCHEM_PKA_STRONGEST_BASIC>
8.548911473751295

> <JCHEM_POLAR_SURFACE_AREA>
53.760000000000005

> <JCHEM_REFRACTIVITY>
92.4556

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(2-ethoxyethyl)-2-(4-methyl-1,4-diazepan-1-yl)-1,3-benzodiazol-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060777
     RDKit          3D
5-Hydroxyemedastine
 49 51  0  0  0  0  0  0  0  0999 V2000
    3.2366    3.4669   -0.4548 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8901    2.7494    0.7316 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9680    1.9194    1.3657 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4895    0.9677    0.4879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4763    0.0663    1.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9488   -0.9388    0.3398 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1532   -0.8608   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1047    0.1507   -0.5489 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0803    1.3584    0.1905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1414    2.3580   -0.3150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5186    1.9279    0.1208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1131    0.9766   -0.7702 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5193    0.8461   -0.4755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4370   -0.3051   -0.7471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1616   -0.1433   -1.5479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2537   -2.0436   -1.0939 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7588   -2.8501   -0.7821 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1454   -4.1267   -1.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2814   -4.7089   -0.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6797   -5.9988   -1.0249 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -3.9755    0.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6843   -2.7191    0.6699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5221   -2.1603    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1528    3.6062   -0.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7714    4.3978   -0.6514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3241    2.7630   -1.3155 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3141    3.4714    1.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7239    2.1323    0.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1139    1.3476   -0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3531    0.2960    0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364   -0.4696    1.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7820    0.6066    1.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1535    1.9062    0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4206    1.2055    1.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0451    2.5504   -1.3824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9159    3.3119    0.2191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1616    2.8297    0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.5517    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9974    1.8122   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9621   -0.0269   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6541    0.8173    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2538   -0.6701    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1372   -1.0278   -1.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9578   -1.0801   -2.0764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2202    0.7139   -2.2580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5139   -4.6312   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3721   -6.8216   -0.5299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9125   -4.4208    0.6754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2356   -2.1280    1.3713 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  7 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 23  6  1  0
 15  8  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 14 43  1  0
 15 44  1  0
 15 45  1  0
 18 46  1  0
 20 47  1  0
 21 48  1  0
 22 49  1  0
M  END

HEADER    PROTEIN                                 04-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-13         0                                  
HETATM    1  C   UNK     0       1.386  -4.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.178 -10.270   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.720  -3.780   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.540  -8.394   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.661   0.361   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.185  -1.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.730  -9.372   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.563  -6.854   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.925  -7.675   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.277  -6.277   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.721  -4.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.387  -3.780   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.198  -0.463   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.167   0.681   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.722  -1.928   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.215  -2.248   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.461  -4.406   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      10.492  -3.261   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      11.236  -9.052   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       9.781  -5.912   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       8.054  -3.780   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       9.643   2.146   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.053  -4.550   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   19                                                            
CONECT    3    1   23                                                       
CONECT    4    7    8                                                       
CONECT    5    6   14                                                       
CONECT    6    5   16                                                       
CONECT    7    4   19                                                       
CONECT    8    4   20                                                       
CONECT    9   10   19                                                       
CONECT   10    9   20                                                       
CONECT   11   12   21                                                       
CONECT   12   11   23                                                       
CONECT   13   14   15                                                       
CONECT   14    5   13   22                                                  
CONECT   15   13   16   18                                                  
CONECT   16    6   15   21                                                  
CONECT   17   18   20   21                                                  
CONECT   18   15   17                                                       
CONECT   19    2    7    9                                                  
CONECT   20    8   10   17                                                  
CONECT   21   11   16   17                                                  
CONECT   22   14                                                            
CONECT   23    3   12                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0060777
HETATM    1  C1  UNL     1       3.237   3.467  -0.455  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.890   2.749   0.732  1.00  0.00           C  
HETATM    3  O1  UNL     1       2.968   1.919   1.366  1.00  0.00           O  
HETATM    4  C3  UNL     1       2.489   0.968   0.488  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.476   0.066   1.212  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.949  -0.939   0.340  1.00  0.00           N  
HETATM    7  C5  UNL     1      -0.153  -0.861  -0.411  1.00  0.00           C  
HETATM    8  N2  UNL     1      -1.105   0.151  -0.549  1.00  0.00           N  
HETATM    9  C6  UNL     1      -1.080   1.358   0.191  1.00  0.00           C  
HETATM   10  C7  UNL     1      -2.141   2.358  -0.315  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.519   1.928   0.121  1.00  0.00           C  
HETATM   12  N3  UNL     1      -4.113   0.977  -0.770  1.00  0.00           N  
HETATM   13  C9  UNL     1      -5.519   0.846  -0.476  1.00  0.00           C  
HETATM   14  C10 UNL     1      -3.437  -0.305  -0.747  1.00  0.00           C  
HETATM   15  C11 UNL     1      -2.162  -0.143  -1.548  1.00  0.00           C  
HETATM   16  N4  UNL     1      -0.254  -2.044  -1.094  1.00  0.00           N  
HETATM   17  C12 UNL     1       0.759  -2.850  -0.782  1.00  0.00           C  
HETATM   18  C13 UNL     1       1.145  -4.127  -1.162  1.00  0.00           C  
HETATM   19  C14 UNL     1       2.281  -4.709  -0.646  1.00  0.00           C  
HETATM   20  O2  UNL     1       2.680  -5.999  -1.025  1.00  0.00           O  
HETATM   21  C15 UNL     1       3.015  -3.975   0.260  1.00  0.00           C  
HETATM   22  C16 UNL     1       2.684  -2.719   0.670  1.00  0.00           C  
HETATM   23  C17 UNL     1       1.522  -2.160   0.122  1.00  0.00           C  
HETATM   24  H1  UNL     1       2.153   3.606  -0.223  1.00  0.00           H  
HETATM   25  H2  UNL     1       3.771   4.398  -0.651  1.00  0.00           H  
HETATM   26  H3  UNL     1       3.324   2.763  -1.315  1.00  0.00           H  
HETATM   27  H4  UNL     1       4.314   3.471   1.433  1.00  0.00           H  
HETATM   28  H5  UNL     1       4.724   2.132   0.334  1.00  0.00           H  
HETATM   29  H6  UNL     1       2.114   1.348  -0.461  1.00  0.00           H  
HETATM   30  H7  UNL     1       3.353   0.296   0.238  1.00  0.00           H  
HETATM   31  H8  UNL     1       2.136  -0.470   1.970  1.00  0.00           H  
HETATM   32  H9  UNL     1       0.782   0.607   1.840  1.00  0.00           H  
HETATM   33  H10 UNL     1      -0.153   1.906   0.070  1.00  0.00           H  
HETATM   34  H11 UNL     1      -1.421   1.205   1.252  1.00  0.00           H  
HETATM   35  H12 UNL     1      -2.045   2.550  -1.382  1.00  0.00           H  
HETATM   36  H13 UNL     1      -1.916   3.312   0.219  1.00  0.00           H  
HETATM   37  H14 UNL     1      -4.162   2.830   0.145  1.00  0.00           H  
HETATM   38  H15 UNL     1      -3.440   1.552   1.162  1.00  0.00           H  
HETATM   39  H16 UNL     1      -5.997   1.812  -0.808  1.00  0.00           H  
HETATM   40  H17 UNL     1      -5.962  -0.027  -0.996  1.00  0.00           H  
HETATM   41  H18 UNL     1      -5.654   0.817   0.622  1.00  0.00           H  
HETATM   42  H19 UNL     1      -3.254  -0.670   0.284  1.00  0.00           H  
HETATM   43  H20 UNL     1      -4.137  -1.028  -1.249  1.00  0.00           H  
HETATM   44  H21 UNL     1      -1.958  -1.080  -2.076  1.00  0.00           H  
HETATM   45  H22 UNL     1      -2.220   0.714  -2.258  1.00  0.00           H  
HETATM   46  H23 UNL     1       0.514  -4.631  -1.877  1.00  0.00           H  
HETATM   47  H24 UNL     1       2.372  -6.822  -0.530  1.00  0.00           H  
HETATM   48  H25 UNL     1       3.912  -4.421   0.675  1.00  0.00           H  
HETATM   49  H26 UNL     1       3.236  -2.128   1.371  1.00  0.00           H  
CONECT    1    2   24   25   26
CONECT    2    3   27   28
CONECT    3    4
CONECT    4    5   29   30
CONECT    5    6   31   32
CONECT    6    7   23
CONECT    7    8   16   16
CONECT    8    9   15
CONECT    9   10   33   34
CONECT   10   11   35   36
CONECT   11   12   37   38
CONECT   12   13   14
CONECT   13   39   40   41
CONECT   14   15   42   43
CONECT   15   44   45
CONECT   16   17
CONECT   17   18   18   23
CONECT   18   19   46
CONECT   19   20   21   21
CONECT   20   47
CONECT   21   22   48
CONECT   22   23   23   49
END

HMDB0060777
     RDKit          3D
5-Hydroxyemedastine
 49 51  0  0  0  0  0  0  0  0999 V2000
    3.2366    3.4669   -0.4548 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8901    2.7494    0.7316 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9680    1.9194    1.3657 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4895    0.9677    0.4879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4763    0.0663    1.2122 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9488   -0.9388    0.3398 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1532   -0.8608   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1047    0.1507   -0.5489 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0803    1.3584    0.1905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1414    2.3580   -0.3150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5186    1.9279    0.1208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1131    0.9766   -0.7702 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5193    0.8461   -0.4755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4370   -0.3051   -0.7471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1616   -0.1433   -1.5479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2537   -2.0436   -1.0939 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7588   -2.8501   -0.7821 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1454   -4.1267   -1.1625 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2814   -4.7089   -0.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6797   -5.9988   -1.0249 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -3.9755    0.2601 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6843   -2.7191    0.6699 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5221   -2.1603    0.1223 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1528    3.6062   -0.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7714    4.3978   -0.6514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3241    2.7630   -1.3155 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3141    3.4714    1.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7239    2.1323    0.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1139    1.3476   -0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3531    0.2960    0.2376 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364   -0.4696    1.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7820    0.6066    1.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1535    1.9062    0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4206    1.2055    1.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0451    2.5504   -1.3824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9159    3.3119    0.2191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1616    2.8297    0.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402    1.5517    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9974    1.8122   -0.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9621   -0.0269   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6541    0.8173    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2538   -0.6701    0.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1372   -1.0278   -1.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9578   -1.0801   -2.0764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2202    0.7139   -2.2580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5139   -4.6312   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3721   -6.8216   -0.5299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9125   -4.4208    0.6754 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2356   -2.1280    1.3713 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  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
  7 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 19 21  2  0
 21 22  1  0
 22 23  2  0
 23  6  1  0
 15  8  1  0
 23 17  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 14 43  1  0
 15 44  1  0
 15 45  1  0
 18 46  1  0
 20 47  1  0
 21 48  1  0
 22 49  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₇H₂₆N₄O₂

Average Molecular Weight

318.4139

Monoisotopic Molecular Weight

318.205576096

IUPAC Name

1-(2-ethoxyethyl)-2-(4-methyl-1,4-diazepan-1-yl)-1H-1,3-benzodiazol-5-ol

Traditional Name

1-(2-ethoxyethyl)-2-(4-methyl-1,4-diazepan-1-yl)-1,3-benzodiazol-5-ol

CAS Registry Number

Not Available

SMILES

CCOCCN1C(=NC2=C1C=CC(O)=C2)N1CCCN(C)CC1

InChI Identifier

InChI=1S/C17H26N4O2/c1-3-23-12-11-21-16-6-5-14(22)13-15(16)18-17(21)20-8-4-7-19(2)9-10-20/h5-6,13,22H,3-4,7-12H2,1-2H3

InChI Key

JNLXTCQXMDMAOC-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
1,4-diazepane
1-hydroxy-2-unsubstituted benzenoid
Diazepane
Aminoimidazole
Benzenoid
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Tertiary aliphatic amine
Tertiary amine
Dialkyl ether
Azacycle
Ether
Amine
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Kidney (HMDB: HMDB0060777)
Liver (HMDB: HMDB0060777)

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060777)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060777)

Cellular substructure

Cytoplasm (HMDB: HMDB0060777)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	2.14 g/L	ALOGPS
logP	2.42	ALOGPS
logP	1.78	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	9.26	ChemAxon
pKa (Strongest Basic)	8.55	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	53.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	92.46 m³·mol⁻¹	ChemAxon
Polarizability	36.6 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	175.165	31661259
DarkChem	[M-H]-	175.005	31661259
DeepCCS	[M+H]+	177.224	30932474
DeepCCS	[M-H]-	174.866	30932474
DeepCCS	[M-2H]-	207.751	30932474
DeepCCS	[M+Na]+	183.317	30932474
AllCCS	[M+H]+	175.5	32859911
AllCCS	[M+H-H2O]+	172.4	32859911
AllCCS	[M+NH4]+	178.3	32859911
AllCCS	[M+Na]+	179.1	32859911
AllCCS	[M-H]-	178.4	32859911
AllCCS	[M+Na-2H]-	178.5	32859911
AllCCS	[M+HCOO]-	178.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxyemedastine	CCOCCN1C(=NC2=C1C=CC(O)=C2)N1CCCN(C)CC1	3687.5	Standard polar	33892256
5-Hydroxyemedastine	CCOCCN1C(=NC2=C1C=CC(O)=C2)N1CCCN(C)CC1	2612.8	Standard non polar	33892256
5-Hydroxyemedastine	CCOCCN1C(=NC2=C1C=CC(O)=C2)N1CCCN(C)CC1	2785.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxyemedastine,1TMS,isomer #1	CCOCCN1C(N2CCCN(C)CC2)=NC2=CC(O[Si](C)(C)C)=CC=C21	2666.3	Semi standard non polar	33892256
5-Hydroxyemedastine,1TBDMS,isomer #1	CCOCCN1C(N2CCCN(C)CC2)=NC2=CC(O[Si](C)(C)C(C)(C)C)=CC=C21	2858.8	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 - 5-Hydroxyemedastine GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bb-6290000000-415f9396d7928e3a4d3e	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxyemedastine GC-MS (1 TMS) - 70eV, Positive	splash10-00or-5309000000-efabce9d0b0b0c728640	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxyemedastine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 10V, Positive-QTOF	splash10-014i-0029000000-712b48aa878c5924d96c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 20V, Positive-QTOF	splash10-00xs-1093000000-8c9d7c65be1595452d69	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 40V, Positive-QTOF	splash10-053r-9260000000-e00797e20d67efbf8034	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 10V, Negative-QTOF	splash10-014i-0039000000-6a63d634202dc093770d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 20V, Negative-QTOF	splash10-00kb-1093000000-1a0a0a3e31c32e883700	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 40V, Negative-QTOF	splash10-0101-2590000000-35bbf9c5b5ef05176e26	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 10V, Positive-QTOF	splash10-014i-0009000000-0cb8fa1317b9e645f171	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 20V, Positive-QTOF	splash10-014i-0079000000-da11a65bc93590acd7da	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 40V, Positive-QTOF	splash10-03di-1920000000-00428bea1d1e382ac381	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 10V, Negative-QTOF	splash10-014i-0039000000-c21984dd2fe2597daf76	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 20V, Negative-QTOF	splash10-0bta-0291000000-1997ae7273292d542daf	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxyemedastine 40V, Negative-QTOF	splash10-00mw-0690000000-bda5a0e3c6858611ae34	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

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

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14356144

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 5-Hydroxyemedastine (HMDB0060777)

MOL for HMDB0060777 (5-Hydroxyemedastine)

3D MOL for HMDB0060777 (5-Hydroxyemedastine)

3D SDF for HMDB0060777 (5-Hydroxyemedastine)

3D-SDF for HMDB0060777 (5-Hydroxyemedastine)

PDB for HMDB0060777 (5-Hydroxyemedastine)

3D PDB for HMDB0060777 (5-Hydroxyemedastine)

SMILES for HMDB0060777 (5-Hydroxyemedastine)

INCHI for HMDB0060777 (5-Hydroxyemedastine)

Structure for HMDB0060777 (5-Hydroxyemedastine)

3D Structure for HMDB0060777 (5-Hydroxyemedastine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra