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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-01-04 22:31:36 UTC

Update Date

2022-07-12 23:01:06 UTC

HMDB ID

HMDB0240742

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Indigo

Description

Indigo (indigo dye or indigotin) is an organic compound with a distinctive blue color. It is an oxindole dimer consisting of two fused oxindole rings. Indoles are compounds which consist of a pyrrole ring fused to benzene to form 2,3-benzopyrrole. Indigo is found in both plants and animals and has been detected in human urine and human tissues (PMID: 11076521 ; PMID: 8667928 ). The natural precursor to indigo is indican, a colorless, water-soluble derivative of the amino acid tryptophan. Indican readily hydrolyzes to release β-D-glucose and indoxyl. Oxidation of indoxyl by CYP450 enzymes in the liver or kidneys can convert indoxyl to indigo (PMID: 11076521 ). Likewise, exposure to air can convert indoxyl to indigo. In addition to the mammalian production of minute amounts of indigo, this chemical can also be recovered in far larger amounts from plants. Historically, indigo has been extracted from the leaves of certain plants of the Indigofera genus, in particular Indigofera tinctoria. Indigofera plants were commonly grown and used throughout the world for the production of indigo dyestuff. This was economically important due to the previous rarity of some blue dyestuffs historically. India was the primary supplier of indigo to Europe as early as the Greco-Roman era. The association of India with indigo is reflected in the Greek word for the dye, indikón. The Romans latinized the term to indicum, which passed into Italian dialect and eventually into English as the word indigo. Most indigo dye produced today is synthetic, constituting several thousand tons each year. It is most commonly associated with the production of denim cloth and blue jeans.

Structure

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

HMDB0240742
     RDKit          3D
Indigo
 30 33  0  0  0  0  0  0  0  0999 V2000
   -1.0277   -0.5481   -2.3945 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4453   -0.3129   -1.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6658   -0.0307   -0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6588    0.0349    0.0539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5274   -0.1757   -1.0470 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696   -0.0268   -0.5554 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1039   -0.1215   -1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2828    0.0635   -0.4915 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2848    0.3533    0.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.4510    1.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8601    0.2644    0.7921 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4664    0.3155    1.2327 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0078    0.5477    2.3731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5726    0.1748    1.0271 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8955    0.0190    0.5003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1251    0.1235    1.1636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3089   -0.0603    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2346   -0.3489   -0.8579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0324   -0.4541   -1.5205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8396   -0.2700   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2795   -0.3957   -2.0281 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0859   -0.3523   -2.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2295   -0.0185   -1.0089 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2288    0.4926    1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0539    0.6793    2.5353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3047    0.3976    2.0180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1583    0.3534    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2821    0.0197    0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1640   -0.4940   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9493   -0.6808   -2.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  2  1  0
 12  4  1  0
 20 15  1  0
 11  6  1  0
  5 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 14 26  1  0
 16 27  1  0
 17 28  1  0
 18 29  1  0
 19 30  1  0
M  END


  Mrv1572004221603382D          

 20 23  0  0  0  0            999 V2000
   -2.8697    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8697    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1552    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1552    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6561    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6561    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4012    2.9750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12  8  2  0  0  0  0
 12 10  1  0  0  0  0
 14 13  2  0  0  0  0
 15  9  1  0  0  0  0
 15 13  1  0  0  0  0
 16 10  1  0  0  0  0
 16 14  1  0  0  0  0
 17 11  1  0  0  0  0
 17 13  1  0  0  0  0
 18 12  1  0  0  0  0
 18 14  1  0  0  0  0
 19 15  2  0  0  0  0
 20 16  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240742

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1\C(NC2=CC=CC=C12)=C1/NC2=CC=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H10N2O2/c19-15-9-5-1-3-7-11(9)17-13(15)14-16(20)10-6-2-4-8-12(10)18-14/h1-8,17-18H/b14-13+

> <INCHI_KEY>
COHYTHOBJLSHDF-BUHFOSPRSA-N

> <FORMULA>
C16H10N2O2

> <MOLECULAR_WEIGHT>
262.268

> <EXACT_MASS>
262.07422757

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
27.816396736336863

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(E)-1H,1'H,3H,3'H-[2,2'-biindolylidene]-3,3'-dione

> <ALOGPS_LOGP>
2.76

> <JCHEM_LOGP>
2.652360567333333

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.440856500166685

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.179343126637933

> <JCHEM_PKA_STRONGEST_BASIC>
-7.642258675977301

> <JCHEM_POLAR_SURFACE_AREA>
58.199999999999996

> <JCHEM_REFRACTIVITY>
80.041

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.05e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(E)-1H,1'H-[2,2'-biindolylidene]-3,3'-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240742
     RDKit          3D
Indigo
 30 33  0  0  0  0  0  0  0  0999 V2000
   -1.0277   -0.5481   -2.3945 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4453   -0.3129   -1.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6658   -0.0307   -0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6588    0.0349    0.0539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5274   -0.1757   -1.0470 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696   -0.0268   -0.5554 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1039   -0.1215   -1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2828    0.0635   -0.4915 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2848    0.3533    0.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.4510    1.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8601    0.2644    0.7921 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4664    0.3155    1.2327 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0078    0.5477    2.3731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5726    0.1748    1.0271 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8955    0.0190    0.5003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1251    0.1235    1.1636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3089   -0.0603    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2346   -0.3489   -0.8579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0324   -0.4541   -1.5205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8396   -0.2700   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2795   -0.3957   -2.0281 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0859   -0.3523   -2.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2295   -0.0185   -1.0089 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2288    0.4926    1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0539    0.6793    2.5353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3047    0.3976    2.0180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1583    0.3534    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2821    0.0197    0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1640   -0.4940   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9493   -0.6808   -2.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  2  1  0
 12  4  1  0
 20 15  1  0
 11  6  1  0
  5 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 14 26  1  0
 16 27  1  0
 17 28  1  0
 18 29  1  0
 19 30  1  0
M  END

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0      -5.357   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.357   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.023   4.383   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.023   1.303   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.689   3.613   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.689   2.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.225   4.089   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -1.225   1.597   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0      -0.749   5.553   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.650   0.132   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1    9                                                       
CONECT    6    2   10                                                       
CONECT    7    3   11                                                       
CONECT    8    4   12                                                       
CONECT    9    5   11   15                                                  
CONECT   10    6   12   16                                                  
CONECT   11    7    9   17                                                  
CONECT   12    8   10   18                                                  
CONECT   13   14   15   17                                                  
CONECT   14   13   16   18                                                  
CONECT   15    9   13   19                                                  
CONECT   16   10   14   20                                                  
CONECT   17   11   13                                                       
CONECT   18   12   14                                                       
CONECT   19   15                                                            
CONECT   20   16                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

COMPND    HMDB0240742
HETATM    1  O1  UNL     1      -1.028  -0.548  -2.395  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.445  -0.313  -1.246  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.666  -0.031  -0.056  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.659   0.035   0.054  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.527  -0.176  -1.047  1.00  0.00           N  
HETATM    6  C4  UNL     1       2.870  -0.027  -0.555  1.00  0.00           C  
HETATM    7  C5  UNL     1       4.104  -0.122  -1.174  1.00  0.00           C  
HETATM    8  C6  UNL     1       5.283   0.063  -0.491  1.00  0.00           C  
HETATM    9  C7  UNL     1       5.285   0.353   0.848  1.00  0.00           C  
HETATM   10  C8  UNL     1       4.067   0.451   1.478  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.860   0.264   0.792  1.00  0.00           C  
HETATM   12  C10 UNL     1       1.466   0.316   1.233  1.00  0.00           C  
HETATM   13  O2  UNL     1       1.008   0.548   2.373  1.00  0.00           O  
HETATM   14  N2  UNL     1      -1.573   0.175   1.027  1.00  0.00           N  
HETATM   15  C11 UNL     1      -2.895   0.019   0.500  1.00  0.00           C  
HETATM   16  C12 UNL     1      -4.125   0.124   1.164  1.00  0.00           C  
HETATM   17  C13 UNL     1      -5.309  -0.060   0.487  1.00  0.00           C  
HETATM   18  C14 UNL     1      -5.235  -0.349  -0.858  1.00  0.00           C  
HETATM   19  C15 UNL     1      -4.032  -0.454  -1.520  1.00  0.00           C  
HETATM   20  C16 UNL     1      -2.840  -0.270  -0.844  1.00  0.00           C  
HETATM   21  H1  UNL     1       1.279  -0.396  -2.028  1.00  0.00           H  
HETATM   22  H2  UNL     1       4.086  -0.352  -2.238  1.00  0.00           H  
HETATM   23  H3  UNL     1       6.229  -0.018  -1.009  1.00  0.00           H  
HETATM   24  H4  UNL     1       6.229   0.493   1.354  1.00  0.00           H  
HETATM   25  H5  UNL     1       4.054   0.679   2.535  1.00  0.00           H  
HETATM   26  H6  UNL     1      -1.305   0.398   2.018  1.00  0.00           H  
HETATM   27  H7  UNL     1      -4.158   0.353   2.231  1.00  0.00           H  
HETATM   28  H8  UNL     1      -6.282   0.020   0.999  1.00  0.00           H  
HETATM   29  H9  UNL     1      -6.164  -0.494  -1.393  1.00  0.00           H  
HETATM   30  H10 UNL     1      -3.949  -0.681  -2.581  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   20
CONECT    3    4    4   14
CONECT    4    5   12
CONECT    5    6   21
CONECT    6    7    7   11
CONECT    7    8   22
CONECT    8    9    9   23
CONECT    9   10   24
CONECT   10   11   11   25
CONECT   11   12
CONECT   12   13   13
CONECT   14   15   26
CONECT   15   16   16   20
CONECT   16   17   27
CONECT   17   18   18   28
CONECT   18   19   29
CONECT   19   20   20   30
END

HMDB0240742
     RDKit          3D
Indigo
 30 33  0  0  0  0  0  0  0  0999 V2000
   -1.0277   -0.5481   -2.3945 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4453   -0.3129   -1.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6658   -0.0307   -0.0559 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6588    0.0349    0.0539 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5274   -0.1757   -1.0470 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696   -0.0268   -0.5554 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1039   -0.1215   -1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2828    0.0635   -0.4915 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2848    0.3533    0.8483 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.4510    1.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8601    0.2644    0.7921 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4664    0.3155    1.2327 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0078    0.5477    2.3731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5726    0.1748    1.0271 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8955    0.0190    0.5003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1251    0.1235    1.1636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3089   -0.0603    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2346   -0.3489   -0.8579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0324   -0.4541   -1.5205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8396   -0.2700   -0.8437 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2795   -0.3957   -2.0281 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0859   -0.3523   -2.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2295   -0.0185   -1.0089 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2288    0.4926    1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0539    0.6793    2.5353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3047    0.3976    2.0180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1583    0.3534    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2821    0.0197    0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1640   -0.4940   -1.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9493   -0.6808   -2.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  3 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20  2  1  0
 12  4  1  0
 20 15  1  0
 11  6  1  0
  5 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 14 26  1  0
 16 27  1  0
 17 28  1  0
 18 29  1  0
 19 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Indigotin	HMDB
Cystoceva	HMDB
Diindogen	HMDB
Vulcafix blue R	HMDB
Indigotindisulfonic acid	HMDB
Indigo carmine	HMDB
Indigotindisulfonate	HMDB
Soluble indigo blue	HMDB
Disulfonate, indigo	HMDB
2-(1,3-Dihydro-3-oxo-5-sulphO-2H-indol-2-ylidene)-3- oxoindoline-5-sulphonic acid	HMDB
FD And C blue no. 2	HMDB
Indigo blue, soluble	HMDB
(delta-2,2'-Biindole)-3,3'-dione	HMDB
D And C blue no. 6	HMDB
Carmine, indigo	HMDB
Indigo disulfonate	HMDB
Indigo blue	HMDB
Indigotindisulfonate sodium	HMDB
Indigo	MeSH

Chemical Formula

C₁₆H₁₀N₂O₂

Average Molecular Weight

262.268

Monoisotopic Molecular Weight

262.07422757

IUPAC Name

(E)-1H,1'H,3H,3'H-[2,2'-biindolylidene]-3,3'-dione

Traditional Name

(E)-1H,1'H-[2,2'-biindolylidene]-3,3'-dione

CAS Registry Number

Not Available

SMILES

O=C1\C(NC2=CC=CC=C12)=C1/NC2=CC=CC=C2C1=O

InChI Identifier

InChI=1S/C16H10N2O2/c19-15-9-5-1-3-7-11(9)17-13(15)14-16(20)10-6-2-4-8-12(10)18-14/h1-8,17-18H/b14-13+

InChI Key

COHYTHOBJLSHDF-BUHFOSPRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolines

Direct Parent

Indolines

Alternative Parents

Substituents

Dihydroindole
Aryl ketone
Secondary aliphatic/aromatic amine
Benzenoid
Vinylogous amide
Ketone
Secondary amine
Enamine
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Amine
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0240742)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.76	ALOGPS
logP	2.65	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.18	ChemAxon
pKa (Strongest Basic)	-7.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	80.04 m³·mol⁻¹	ChemAxon
Polarizability	27.82 Å³	ChemAxon
Number of Rings	4	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
DeepCCS	[M-2H]-	188.843	30932474
DeepCCS	[M+Na]+	164.322	30932474
AllCCS	[M+H]+	161.4	32859911
AllCCS	[M+H-H2O]+	157.7	32859911
AllCCS	[M+NH4]+	164.7	32859911
AllCCS	[M+Na]+	165.7	32859911
AllCCS	[M-H]-	162.5	32859911
AllCCS	[M+Na-2H]-	161.5	32859911
AllCCS	[M+HCOO]-	160.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	13.6599 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.44 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2184.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	385.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	116.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	203.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	106.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	467.4 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	737.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	145.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1069.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	430.9 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	1552.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	489.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	390.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	524.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	160.5 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	177.0 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Indigo	O=C1\C(NC2=CC=CC=C12)=C1/NC2=CC=CC=C2C1=O	3959.4	Standard polar	33892256
Indigo	O=C1\C(NC2=CC=CC=C12)=C1/NC2=CC=CC=C2C1=O	2943.5	Standard non polar	33892256
Indigo	O=C1\C(NC2=CC=CC=C12)=C1/NC2=CC=CC=C2C1=O	2961.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Indigo,1TMS,isomer #1	C[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	2773.0	Semi standard non polar	33892256
Indigo,1TMS,isomer #1	C[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	2701.1	Standard non polar	33892256
Indigo,1TMS,isomer #1	C[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	4403.2	Standard polar	33892256
Indigo,2TMS,isomer #1	C[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C(=O)C2=CC=CC=C21	2657.8	Semi standard non polar	33892256
Indigo,2TMS,isomer #1	C[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C(=O)C2=CC=CC=C21	2691.4	Standard non polar	33892256
Indigo,2TMS,isomer #1	C[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C(=O)C2=CC=CC=C21	3369.4	Standard polar	33892256
Indigo,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	3068.5	Semi standard non polar	33892256
Indigo,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	2915.3	Standard non polar	33892256
Indigo,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2/NC3=CC=CC=C3C2=O)C(=O)C2=CC=CC=C21	4445.3	Standard polar	33892256
Indigo,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C(=O)C2=CC=CC=C21	3151.1	Semi standard non polar	33892256
Indigo,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C(=O)C2=CC=CC=C21	3080.7	Standard non polar	33892256
Indigo,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C(=O)C2=CC=CC=C21	3439.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Indigo 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 - Indigo 10V, Positive-QTOF	splash10-03di-0090000000-790509310d3a9b1089dc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 20V, Positive-QTOF	splash10-03di-0290000000-b87193ec33d05c5972bc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 40V, Positive-QTOF	splash10-0006-1920000000-06f522bb3b9294630d21	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 10V, Negative-QTOF	splash10-03di-0090000000-7b4ca08a5827f92042b5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 20V, Negative-QTOF	splash10-03di-0290000000-8e31bd790d0c838bafde	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 40V, Negative-QTOF	splash10-001i-0590000000-1d3c68663ee4df12a0e2	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 10V, Negative-QTOF	splash10-03di-0090000000-fc429704171183f86ba8	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 20V, Negative-QTOF	splash10-03di-0290000000-8d486152aa8dcd21f192	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 40V, Negative-QTOF	splash10-001i-0920000000-4c6f54d2c5462973f105	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 10V, Positive-QTOF	splash10-03di-0090000000-d2ff69a7f2ebf2ad3717	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 20V, Positive-QTOF	splash10-03e9-0690000000-024cece7c516595caa9f	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indigo 40V, Positive-QTOF	splash10-0w30-0960000000-2d6f1d15e9a51ab8b9f5	2021-09-25	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

C00000126

Chemspider ID

4477009

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Indigo

METLIN ID

Not Available

PubChem Compound

5318432

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

Gillam EM, Notley LM, Cai H, De Voss JJ, Guengerich FP: Oxidation of indole by cytochrome P450 enzymes. Biochemistry. 2000 Nov 14;39(45):13817-24. doi: 10.1021/bi001229u. [PubMed:11076521 ]
Arnold WN: King George III's urine and indigo blue. Lancet. 1996 Jun 29;347(9018):1811-3. doi: 10.1016/s0140-6736(96)91622-0. [PubMed:8667928 ]

Enzymes

Enzyme Details

1. Aryl hydrocarbon receptor

General function:: Involved in transcription regulator activity
Specific function:: Ligand-activated transcriptional activator. Binds to the XRE promoter region of genes it activates. Activates the expression of multiple phase I and II xenobiotic chemical metabolizing enzyme genes (such as the CYP1A1 gene). Mediates biochemical and toxic effects of halogenated aromatic hydrocarbons. Involved in cell-cycle regulation. Likely to play an important role in the development and maturation of many tissues
Gene Name:: AHR
Uniprot ID:: P35869
Molecular weight:: 96146.7

Showing metabocard for Indigo (HMDB0240742)

MOL for HMDB0240742 (Indigo)

3D MOL for HMDB0240742 (Indigo)

3D SDF for HMDB0240742 (Indigo)

3D-SDF for HMDB0240742 (Indigo)

PDB for HMDB0240742 (Indigo)

3D PDB for HMDB0240742 (Indigo)

SMILES for HMDB0240742 (Indigo)

INCHI for HMDB0240742 (Indigo)

Structure for HMDB0240742 (Indigo)

3D Structure for HMDB0240742 (Indigo)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes