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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-05-09 20:52:18 UTC

Update Date

2022-03-07 03:17:38 UTC

HMDB ID

HMDB0060069

Secondary Accession Numbers

HMDB60069

Metabolite Identification

Common Name

cyclic 3-Hydroxymelatonin

Description

cyclic 3-Hydroxymelatonin belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. cyclic 3-Hydroxymelatonin is a moderately basic compound (based on its pKa).

Structure

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

HMDB0060069
     RDKit          3D
cyclic 3-Hydroxymelatonin
 34 36  0  0  0  0  0  0  0  0999 V2000
   -5.6354    0.2765   -0.3198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4214    0.6289   -0.9410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2276    0.1557   -0.4257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1943   -0.6565    0.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9888   -1.1086    1.1714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7840   -0.7536    0.5477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8663    0.0570   -0.5566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0605    0.5117   -1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5301    0.2681   -1.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6781    0.2860   -2.3695 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0560    1.5165   -0.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5432    1.2307   -0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.1893   -0.0297 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -0.8492    0.4293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0368   -0.1335    0.7010 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7438   -2.0894    0.6209 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3423   -0.8027   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5687   -1.0812    0.8473 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8336   -0.8029   -0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4279    0.9182   -0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5894    0.4896    0.7759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1457   -0.9081    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9544   -1.7453    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0986    1.1545   -1.9252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5050   -0.6192   -2.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712    1.5193    0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8167    2.4275   -0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9774    1.8090    0.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9881    1.4568   -1.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8763   -0.8042    0.4665 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0349    0.2194    1.7571 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1369    0.7953    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4345   -1.7266   -0.9205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981   -1.4501    1.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 13 17  1  0
 17 18  1  0
  8  3  1  0
 17  9  1  0
 18  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 15 30  1  0
 15 31  1  0
 15 32  1  0
 17 33  1  0
 18 34  1  0
M  END


  Mrv0541 05091313522D          

 18 20  0  0  0  0            999 V2000
    1.1751    2.1948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1467    0.0632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0186    1.2673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4546    1.8694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9292    0.3783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2523    0.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9758    0.2904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9938    2.2972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7792    0.4778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4118    0.8925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6512    1.6820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3166    1.6557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5869    0.8763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9743    2.1537    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4917    1.6395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3144    3.0573    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8573    0.0968    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3432   -0.1242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  6  5  1  0  0  0  0
  8  1  1  0  0  0  0
  9  3  1  0  0  0  0
  9  7  2  0  0  0  0
 10  7  1  0  0  0  0
 11  4  1  0  0  0  0
 11 10  2  0  0  0  0
 13  5  1  0  0  0  0
 13 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15  6  1  0  0  0  0
 15  8  1  0  0  0  0
 15 12  1  0  0  0  0
 16  8  2  0  0  0  0
 17 13  1  0  0  0  0
 18  2  1  0  0  0  0
 18  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060069

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C(NC3N(CCC23O)C(C)=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C13H16N2O3/c1-8(16)15-6-5-13(17)10-7-9(18-2)3-4-11(10)14-12(13)15/h3-4,7,12,14,17H,5-6H2,1-2H3

> <INCHI_KEY>
VADOSKJWFKUPQF-UHFFFAOYSA-N

> <FORMULA>
C13H16N2O3

> <MOLECULAR_WEIGHT>
248.2777

> <EXACT_MASS>
248.116092388

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
25.623067499870068

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-{3a-hydroxy-5-methoxy-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-1-yl}ethan-1-one

> <ALOGPS_LOGP>
0.67

> <JCHEM_LOGP>
-0.20713452333333277

> <ALOGPS_LOGS>
-1.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.429070667920502

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.004028145839769

> <JCHEM_PKA_STRONGEST_BASIC>
1.9122664614430658

> <JCHEM_POLAR_SURFACE_AREA>
61.80000000000001

> <JCHEM_REFRACTIVITY>
67.04600000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-{3a-hydroxy-5-methoxy-2H,3H,8H,8aH-pyrrolo[2,3-b]indol-1-yl}ethanone

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060069
     RDKit          3D
cyclic 3-Hydroxymelatonin
 34 36  0  0  0  0  0  0  0  0999 V2000
   -5.6354    0.2765   -0.3198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4214    0.6289   -0.9410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2276    0.1557   -0.4257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1943   -0.6565    0.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9888   -1.1086    1.1714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7840   -0.7536    0.5477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8663    0.0570   -0.5566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0605    0.5117   -1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5301    0.2681   -1.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6781    0.2860   -2.3695 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0560    1.5165   -0.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5432    1.2307   -0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.1893   -0.0297 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -0.8492    0.4293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0368   -0.1335    0.7010 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7438   -2.0894    0.6209 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3423   -0.8027   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5687   -1.0812    0.8473 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8336   -0.8029   -0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4279    0.9182   -0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5894    0.4896    0.7759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1457   -0.9081    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9544   -1.7453    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0986    1.1545   -1.9252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5050   -0.6192   -2.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712    1.5193    0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8167    2.4275   -0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9774    1.8090    0.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9881    1.4568   -1.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8763   -0.8042    0.4665 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0349    0.2194    1.7571 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1369    0.7953    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4345   -1.7266   -0.9205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981   -1.4501    1.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 13 17  1  0
 17 18  1  0
  8  3  1  0
 17  9  1  0
 18  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 15 30  1  0
 15 31  1  0
 15 32  1  0
 17 33  1  0
 18 34  1  0
M  END

HEADER    PROTEIN                                 09-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-MAY-13         0                                  
HETATM    1  C   UNK     0       2.194   4.097   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.341   0.118   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.235   2.366   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.182   3.490   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.468   0.706   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.204   1.587   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.288   0.542   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.722   4.288   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.788   0.892   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.235   1.666   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.682   3.140   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.191   3.091   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.696   1.636   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       7.419   4.020   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       4.651   3.060   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       4.320   5.707   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.200   0.181   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      11.841  -0.232   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2   18                                                            
CONECT    3    4    9                                                       
CONECT    4    3   11                                                       
CONECT    5    6   13                                                       
CONECT    6    5   15                                                       
CONECT    7    9   10                                                       
CONECT    8    1   15   16                                                  
CONECT    9    3    7   18                                                  
CONECT   10    7   11   13                                                  
CONECT   11    4   10   14                                                  
CONECT   12   13   14   15                                                  
CONECT   13    5   10   12   17                                             
CONECT   14   11   12                                                       
CONECT   15    6    8   12                                                  
CONECT   16    8                                                            
CONECT   17   13                                                            
CONECT   18    2    9                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0060069
HETATM    1  C1  UNL     1      -5.635   0.276  -0.320  1.00  0.00           C  
HETATM    2  O1  UNL     1      -4.421   0.629  -0.941  1.00  0.00           O  
HETATM    3  C2  UNL     1      -3.228   0.156  -0.426  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.194  -0.656   0.686  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.989  -1.109   1.171  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.784  -0.754   0.548  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.866   0.057  -0.557  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.060   0.512  -1.046  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.530   0.268  -1.007  1.00  0.00           C  
HETATM   10  O2  UNL     1       0.678   0.286  -2.370  1.00  0.00           O  
HETATM   11  C9  UNL     1       1.056   1.517  -0.333  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.543   1.231  -0.282  1.00  0.00           C  
HETATM   13  N1  UNL     1       2.619  -0.189  -0.030  1.00  0.00           N  
HETATM   14  C11 UNL     1       3.771  -0.849   0.429  1.00  0.00           C  
HETATM   15  C12 UNL     1       5.037  -0.134   0.701  1.00  0.00           C  
HETATM   16  O3  UNL     1       3.744  -2.089   0.621  1.00  0.00           O  
HETATM   17  C13 UNL     1       1.342  -0.803  -0.321  1.00  0.00           C  
HETATM   18  N2  UNL     1       0.569  -1.081   0.847  1.00  0.00           N  
HETATM   19  H1  UNL     1      -5.834  -0.803  -0.477  1.00  0.00           H  
HETATM   20  H2  UNL     1      -6.428   0.918  -0.782  1.00  0.00           H  
HETATM   21  H3  UNL     1      -5.589   0.490   0.776  1.00  0.00           H  
HETATM   22  H4  UNL     1      -4.146  -0.908   1.139  1.00  0.00           H  
HETATM   23  H5  UNL     1      -1.954  -1.745   2.042  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.099   1.154  -1.925  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.505  -0.619  -2.713  1.00  0.00           H  
HETATM   26  H8  UNL     1       0.671   1.519   0.703  1.00  0.00           H  
HETATM   27  H9  UNL     1       0.817   2.427  -0.891  1.00  0.00           H  
HETATM   28  H10 UNL     1       2.977   1.809   0.540  1.00  0.00           H  
HETATM   29  H11 UNL     1       2.988   1.457  -1.271  1.00  0.00           H  
HETATM   30  H12 UNL     1       5.876  -0.804   0.467  1.00  0.00           H  
HETATM   31  H13 UNL     1       5.035   0.219   1.757  1.00  0.00           H  
HETATM   32  H14 UNL     1       5.137   0.795   0.074  1.00  0.00           H  
HETATM   33  H15 UNL     1       1.434  -1.727  -0.921  1.00  0.00           H  
HETATM   34  H16 UNL     1       0.898  -1.450   1.752  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   22
CONECT    5    6    6   23
CONECT    6    7   18
CONECT    7    8    8    9
CONECT    8   24
CONECT    9   10   11   17
CONECT   10   25
CONECT   11   12   26   27
CONECT   12   13   28   29
CONECT   13   14   17
CONECT   14   15   16   16
CONECT   15   30   31   32
CONECT   17   18   33
CONECT   18   34
END

HMDB0060069
     RDKit          3D
cyclic 3-Hydroxymelatonin
 34 36  0  0  0  0  0  0  0  0999 V2000
   -5.6354    0.2765   -0.3198 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4214    0.6289   -0.9410 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2276    0.1557   -0.4257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1943   -0.6565    0.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9888   -1.1086    1.1714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7840   -0.7536    0.5477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8663    0.0570   -0.5566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0605    0.5117   -1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5301    0.2681   -1.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6781    0.2860   -2.3695 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0560    1.5165   -0.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5432    1.2307   -0.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.1893   -0.0297 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7712   -0.8492    0.4293 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0368   -0.1335    0.7010 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7438   -2.0894    0.6209 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3423   -0.8027   -0.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5687   -1.0812    0.8473 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8336   -0.8029   -0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4279    0.9182   -0.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5894    0.4896    0.7759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1457   -0.9081    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9544   -1.7453    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0986    1.1545   -1.9252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5050   -0.6192   -2.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712    1.5193    0.7028 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8167    2.4275   -0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9774    1.8090    0.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9881    1.4568   -1.2715 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8763   -0.8042    0.4665 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0349    0.2194    1.7571 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1369    0.7953    0.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4345   -1.7266   -0.9205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8981   -1.4501    1.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  2  0
 13 17  1  0
 17 18  1  0
  8  3  1  0
 17  9  1  0
 18  6  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  5 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 12 28  1  0
 12 29  1  0
 15 30  1  0
 15 31  1  0
 15 32  1  0
 17 33  1  0
 18 34  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₃H₁₆N₂O₃

Average Molecular Weight

248.2777

Monoisotopic Molecular Weight

248.116092388

IUPAC Name

1-{3a-hydroxy-5-methoxy-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-1-yl}ethan-1-one

Traditional Name

1-{3a-hydroxy-5-methoxy-2H,3H,8H,8aH-pyrrolo[2,3-b]indol-1-yl}ethanone

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(NC3N(CCC23O)C(C)=O)C=C1

InChI Identifier

InChI=1S/C13H16N2O3/c1-8(16)15-6-5-13(17)10-7-9(18-2)3-4-11(10)14-12(13)15/h3-4,7,12,14,17H,5-6H2,1-2H3

InChI Key

VADOSKJWFKUPQF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyrroloindoles

Direct Parent

Pyrroloindoles

Alternative Parents

Substituents

Pyrroloindole
Indole
Dihydroindole
Anisole
N-acylpyrrolidine
Alkyl aryl ether
Secondary aliphatic/aromatic amine
Benzenoid
Pyrrole
Pyrrolidine
Acetamide
Tertiary alcohol
Tertiary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Secondary amine
Azacycle
Carboxylic acid derivative
Ether
Organopnictogen compound
Amine
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Not Available

Not Available

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	10.5 g/L	ALOGPS
logP	0.67	ALOGPS
logP	-0.21	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13	ChemAxon
pKa (Strongest Basic)	1.91	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	61.8 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	67.05 m³·mol⁻¹	ChemAxon
Polarizability	25.62 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]+	157.388	31661259
DarkChem	[M-H]-	156.303	31661259
DeepCCS	[M-2H]-	191.056	30932474
DeepCCS	[M+Na]+	166.621	30932474
AllCCS	[M+H]+	156.5	32859911
AllCCS	[M+H-H2O]+	152.7	32859911
AllCCS	[M+NH4]+	160.0	32859911
AllCCS	[M+Na]+	161.0	32859911
AllCCS	[M-H]-	161.2	32859911
AllCCS	[M+Na-2H]-	161.1	32859911
AllCCS	[M+HCOO]-	161.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
cyclic 3-Hydroxymelatonin	COC1=CC2=C(NC3N(CCC23O)C(C)=O)C=C1	3671.1	Standard polar	33892256
cyclic 3-Hydroxymelatonin	COC1=CC2=C(NC3N(CCC23O)C(C)=O)C=C1	2252.4	Standard non polar	33892256
cyclic 3-Hydroxymelatonin	COC1=CC2=C(NC3N(CCC23O)C(C)=O)C=C1	2384.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
cyclic 3-Hydroxymelatonin,1TMS,isomer #1	COC1=CC=C2NC3N(C(C)=O)CCC3(O[Si](C)(C)C)C2=C1	2328.4	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,1TMS,isomer #2	COC1=CC=C2C(=C1)C1(O)CCN(C(C)=O)C1N2[Si](C)(C)C	2273.4	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C	2287.0	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C	2204.1	Standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C	2628.2	Standard polar	33892256
cyclic 3-Hydroxymelatonin,1TBDMS,isomer #1	COC1=CC=C2NC3N(C(C)=O)CCC3(O[Si](C)(C)C(C)(C)C)C2=C1	2571.0	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,1TBDMS,isomer #2	COC1=CC=C2C(=C1)C1(O)CCN(C(C)=O)C1N2[Si](C)(C)C(C)(C)C	2547.2	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TBDMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C(C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C(C)(C)C	2755.5	Semi standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TBDMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C(C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C(C)(C)C	2696.5	Standard non polar	33892256
cyclic 3-Hydroxymelatonin,2TBDMS,isomer #1	COC1=CC=C2C(=C1)C1(O[Si](C)(C)C(C)(C)C)CCN(C(C)=O)C1N2[Si](C)(C)C(C)(C)C	2856.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - cyclic 3-Hydroxymelatonin GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-1920000000-d9480054221e25bb27e8	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cyclic 3-Hydroxymelatonin GC-MS (1 TMS) - 70eV, Positive	splash10-00e9-4191000000-cc7a5237ee02233fa4a9	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - cyclic 3-Hydroxymelatonin 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 - cyclic 3-Hydroxymelatonin 10V, Positive-QTOF	splash10-0a4j-0090000000-7c7286c5d8bfe91b2751	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 20V, Positive-QTOF	splash10-0a4i-0690000000-e6bb77b8c9434f4ce36a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 40V, Positive-QTOF	splash10-000l-1900000000-49cd1cd77abdb506c358	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 10V, Negative-QTOF	splash10-052b-0090000000-33a11534cefc1d89b070	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 20V, Negative-QTOF	splash10-052r-0980000000-8195567db4a7a8ff6da6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 40V, Negative-QTOF	splash10-052s-3910000000-0c90de6b946e8d2b674e	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 10V, Positive-QTOF	splash10-0002-0090000000-4f605167774fac2617f5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 20V, Positive-QTOF	splash10-0002-0290000000-a4edec929df35b15c9e6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 40V, Positive-QTOF	splash10-0a4i-0920000000-0147e30a97cc852502b0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 10V, Negative-QTOF	splash10-000b-0390000000-5a18748f93ad930ec230	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 20V, Negative-QTOF	splash10-0a4i-0390000000-bd642bb677898a9ccf27	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - cyclic 3-Hydroxymelatonin 40V, Negative-QTOF	splash10-01qd-6920000000-bdb39f9c23a7e297a65b	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

85950298

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

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]

Showing metabocard for cyclic 3-Hydroxymelatonin (HMDB0060069)

MOL for HMDB0060069 (cyclic 3-Hydroxymelatonin)

3D MOL for HMDB0060069 (cyclic 3-Hydroxymelatonin)

3D SDF for HMDB0060069 (cyclic 3-Hydroxymelatonin)

3D-SDF for HMDB0060069 (cyclic 3-Hydroxymelatonin)

PDB for HMDB0060069 (cyclic 3-Hydroxymelatonin)

3D PDB for HMDB0060069 (cyclic 3-Hydroxymelatonin)

SMILES for HMDB0060069 (cyclic 3-Hydroxymelatonin)

INCHI for HMDB0060069 (cyclic 3-Hydroxymelatonin)

Structure for HMDB0060069 (cyclic 3-Hydroxymelatonin)

3D Structure for HMDB0060069 (cyclic 3-Hydroxymelatonin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra