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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-01-04 22:31:42 UTC

Update Date

2022-09-22 18:34:33 UTC

HMDB ID

HMDB0240743

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Indirubin

Description

Indirubin or indigo red is an organic compound with a distinctive deep red/orange 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. Indirubin is found in both plants and animals and has been detected in human urine and human tissues (PMID: 11076521 ; PMID: 8667928 ). The precursor to indirubin is indican, a colorless, water-soluble derivative of the amino acid tryptophan which is converted to indole via microbial metabolism. 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 indirubin (PMID: 11076521 ). Likewise, exposure to air can convert indoxyl to indirubin. In addition to the mammalian production of minute amounts of indirubin, this chemical can also be recovered in far larger amounts from plants. Historically, indirubin 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 dyes. Indirubin is a chemical constituent of indigo naturalis (also known as qing dai), which has been used for hundreds of years in traditional Chinese medicine. It is produced by collecting the waste products from the bacterial degradation of specific forms of vegetation. Indirubin has shown anti-inflammatory and anti-angiogenesis properties in vitro (PMID: 21207415 ). It has also been studied for potential use in the treatment of ulcerative colitis (PMID: 23674882 ).

Structure

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

HMDB0240743
     RDKit          3D
Indirubin
 30 33  0  0  0  0  0  0  0  0999 V2000
   -0.6782   -3.3668   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2614   -2.2891   -0.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7006   -2.2690   -0.3233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1466   -0.9271   -0.1843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4609   -0.4870   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6530    0.8694    0.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6139    1.7271    0.0880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.2768    0.0338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0720   -0.0679   -0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8704   -0.9016   -0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3949   -0.5083   -0.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8604    0.8325   -0.0319 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3143    0.7885   -0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2245    1.8465    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741    1.5696    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9937    0.2674   -0.1162 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0862   -0.7681   -0.2153 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7263   -0.5074   -0.1800 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610   -1.3750   -0.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5966   -2.5958   -0.3845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3342   -3.1219   -0.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3006   -1.1729   -0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6739    1.2295    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    2.8159    0.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5083    2.0050    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3380    1.7198    0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8842    2.8667    0.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3340    2.3407    0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0402   -0.0123   -0.1514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4003   -1.7852   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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  1  0
 13 14  2  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
 10  2  1  0
 19 11  1  0
  9  4  1  0
 18 13  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
 12 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END


  Mrv1533004241511322D          

 20 23  0  0  0  0            999 V2000
   -0.4012   -2.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6561   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4407   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0538    0.2666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8823    1.0736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0977    1.3285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4846    0.7765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6561   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    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
    2.6378   -1.5229    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
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
 11 19  1  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240743

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NC2=CC=CC=C2\C1=C1/NC2=CC=CC=C2C1=O

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

> <INCHI_KEY>
CRDNMYFJWFXOCH-BUHFOSPRSA-N

> <FORMULA>
C16H10N2O2

> <MOLECULAR_WEIGHT>
262.268

> <EXACT_MASS>
262.07422757

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
27.40792675038748

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2E)-3-oxo-2,3-dihydro-1H-indol-2-ylidene]-2,3-dihydro-1H-indol-2-one

> <ALOGPS_LOGP>
3.05

> <JCHEM_LOGP>
2.4348669949999997

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.69391568801743

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.419850049798394

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5562406765394745

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
78.99539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.47e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2E)-3-oxo-1H-indol-2-ylidene]-1H-indol-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240743
     RDKit          3D
Indirubin
 30 33  0  0  0  0  0  0  0  0999 V2000
   -0.6782   -3.3668   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2614   -2.2891   -0.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7006   -2.2690   -0.3233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1466   -0.9271   -0.1843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4609   -0.4870   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6530    0.8694    0.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6139    1.7271    0.0880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.2768    0.0338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0720   -0.0679   -0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8704   -0.9016   -0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3949   -0.5083   -0.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8604    0.8325   -0.0319 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3143    0.7885   -0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2245    1.8465    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741    1.5696    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9937    0.2674   -0.1162 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0862   -0.7681   -0.2153 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7263   -0.5074   -0.1800 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610   -1.3750   -0.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5966   -2.5958   -0.3845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3342   -3.1219   -0.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3006   -1.1729   -0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6739    1.2295    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    2.8159    0.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5083    2.0050    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3380    1.7198    0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8842    2.8667    0.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3340    2.3407    0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0402   -0.0123   -0.1514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4003   -1.7852   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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  1  0
 13 14  2  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
 10  2  1  0
 19 11  1  0
  9  4  1  0
 18 13  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
 12 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0      -0.749  -4.013   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.225  -2.549   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.689  -2.073   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.689  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.834   0.498   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.514   2.004   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.049   2.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.905   1.449   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.225  -0.057   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.320  -1.303   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9    2   11                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13   19                                                  
CONECT   19   18   11   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   46    0
END

COMPND    HMDB0240743
HETATM    1  O1  UNL     1      -0.678  -3.367  -0.448  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.261  -2.289  -0.335  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.701  -2.269  -0.323  1.00  0.00           N  
HETATM    4  C2  UNL     1      -3.147  -0.927  -0.184  1.00  0.00           C  
HETATM    5  C3  UNL     1      -4.461  -0.487  -0.131  1.00  0.00           C  
HETATM    6  C4  UNL     1      -4.653   0.869   0.008  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.614   1.727   0.088  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.305   1.277   0.034  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.072  -0.068  -0.104  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.870  -0.902  -0.197  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.395  -0.508  -0.165  1.00  0.00           C  
HETATM   12  N2  UNL     1       0.860   0.832  -0.032  1.00  0.00           N  
HETATM   13  C10 UNL     1       2.314   0.788  -0.046  1.00  0.00           C  
HETATM   14  C11 UNL     1       3.224   1.846   0.056  1.00  0.00           C  
HETATM   15  C12 UNL     1       4.574   1.570   0.019  1.00  0.00           C  
HETATM   16  C13 UNL     1       4.994   0.267  -0.116  1.00  0.00           C  
HETATM   17  C14 UNL     1       4.086  -0.768  -0.215  1.00  0.00           C  
HETATM   18  C15 UNL     1       2.726  -0.507  -0.180  1.00  0.00           C  
HETATM   19  C16 UNL     1       1.561  -1.375  -0.260  1.00  0.00           C  
HETATM   20  O2  UNL     1       1.597  -2.596  -0.385  1.00  0.00           O  
HETATM   21  H1  UNL     1      -3.334  -3.122  -0.406  1.00  0.00           H  
HETATM   22  H2  UNL     1      -5.301  -1.173  -0.195  1.00  0.00           H  
HETATM   23  H3  UNL     1      -5.674   1.229   0.051  1.00  0.00           H  
HETATM   24  H4  UNL     1      -3.750   2.816   0.199  1.00  0.00           H  
HETATM   25  H5  UNL     1      -1.508   2.005   0.102  1.00  0.00           H  
HETATM   26  H6  UNL     1       0.338   1.720   0.061  1.00  0.00           H  
HETATM   27  H7  UNL     1       2.884   2.867   0.161  1.00  0.00           H  
HETATM   28  H8  UNL     1       5.334   2.341   0.092  1.00  0.00           H  
HETATM   29  H9  UNL     1       6.040  -0.012  -0.151  1.00  0.00           H  
HETATM   30  H10 UNL     1       4.400  -1.785  -0.321  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   21
CONECT    4    5    5    9
CONECT    5    6   22
CONECT    6    7    7   23
CONECT    7    8   24
CONECT    8    9    9   25
CONECT    9   10
CONECT   10   11   11
CONECT   11   12   19
CONECT   12   13   26
CONECT   13   14   14   18
CONECT   14   15   27
CONECT   15   16   16   28
CONECT   16   17   29
CONECT   17   18   18   30
CONECT   18   19
CONECT   19   20   20
END

HMDB0240743
     RDKit          3D
Indirubin
 30 33  0  0  0  0  0  0  0  0999 V2000
   -0.6782   -3.3668   -0.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2614   -2.2891   -0.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7006   -2.2690   -0.3233 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1466   -0.9271   -0.1843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4609   -0.4870   -0.1311 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6530    0.8694    0.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6139    1.7271    0.0880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3048    1.2768    0.0338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0720   -0.0679   -0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8704   -0.9016   -0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3949   -0.5083   -0.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8604    0.8325   -0.0319 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3143    0.7885   -0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2245    1.8465    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741    1.5696    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9937    0.2674   -0.1162 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0862   -0.7681   -0.2153 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7263   -0.5074   -0.1800 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610   -1.3750   -0.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5966   -2.5958   -0.3845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3342   -3.1219   -0.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3006   -1.1729   -0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6739    1.2295    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7500    2.8159    0.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5083    2.0050    0.1024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3380    1.7198    0.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8842    2.8667    0.1612 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3340    2.3407    0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0402   -0.0123   -0.1514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4003   -1.7852   -0.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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  1  0
 13 14  2  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
 10  2  1  0
 19 11  1  0
  9  4  1  0
 18 13  1  0
  3 21  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
 12 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₆H₁₀N₂O₂

Average Molecular Weight

262.268

Monoisotopic Molecular Weight

262.07422757

IUPAC Name

3-[(2E)-3-oxo-2,3-dihydro-1H-indol-2-ylidene]-2,3-dihydro-1H-indol-2-one

Traditional Name

3-[(2E)-3-oxo-1H-indol-2-ylidene]-1H-indol-2-one

CAS Registry Number

Not Available

SMILES

O=C1NC2=CC=CC=C2\C1=C1/NC2=CC=CC=C2C1=O

InChI Identifier

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

InChI Key

CRDNMYFJWFXOCH-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
Benzenoid
Vinylogous amide
Amino acid or derivatives
Carboxamide group
Ketone
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Enamine
Secondary amine
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Amine
Aldehyde
Organic oxygen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0240743)

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	3.05	ALOGPS
logP	2.43	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	7.42	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	79 m³·mol⁻¹	ChemAxon
Polarizability	27.41 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+H]+	156.278	30932474
DeepCCS	[M-H]-	153.904	30932474
DeepCCS	[M-2H]-	186.882	30932474
DeepCCS	[M+Na]+	162.355	30932474
AllCCS	[M+H]+	161.0	32859911
AllCCS	[M+H-H2O]+	157.1	32859911
AllCCS	[M+NH4]+	164.7	32859911
AllCCS	[M+Na]+	165.8	32859911
AllCCS	[M-H]-	164.5	32859911
AllCCS	[M+Na-2H]-	163.6	32859911
AllCCS	[M+HCOO]-	162.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	12.6647 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.14 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2055.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	353.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	124.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	189.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	82.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	419.5 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	746.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	112.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1017.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	398.7 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	1415.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	417.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	368.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	422.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	151.6 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	130.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Indirubin	O=C1NC2=CC=CC=C2\C1=C1/NC2=CC=CC=C2C1=O	4162.8	Standard polar	33892256
Indirubin	O=C1NC2=CC=CC=C2\C1=C1/NC2=CC=CC=C2C1=O	2975.9	Standard non polar	33892256
Indirubin	O=C1NC2=CC=CC=C2\C1=C1/NC2=CC=CC=C2C1=O	3018.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Indirubin,1TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	2790.2	Semi standard non polar	33892256
Indirubin,1TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	2680.6	Standard non polar	33892256
Indirubin,1TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	4198.2	Standard polar	33892256
Indirubin,1TMS,isomer #2	C[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	2832.1	Semi standard non polar	33892256
Indirubin,1TMS,isomer #2	C[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	2685.7	Standard non polar	33892256
Indirubin,1TMS,isomer #2	C[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	3772.9	Standard polar	33892256
Indirubin,2TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C2=CC=CC=C21	2597.2	Semi standard non polar	33892256
Indirubin,2TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C2=CC=CC=C21	2654.5	Standard non polar	33892256
Indirubin,2TMS,isomer #1	C[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C)C2=CC=CC=C21	3203.0	Standard polar	33892256
Indirubin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	3043.9	Semi standard non polar	33892256
Indirubin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	2893.9	Standard non polar	33892256
Indirubin,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2/NC3=CC=CC=C3C2=O)C2=CC=CC=C21	4253.3	Standard polar	33892256
Indirubin,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	3102.7	Semi standard non polar	33892256
Indirubin,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	2894.5	Standard non polar	33892256
Indirubin,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1/C(=C2/C(=O)NC3=CC=CC=C23)C(=O)C2=CC=CC=C21	3816.5	Standard polar	33892256
Indirubin,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	3113.1	Semi standard non polar	33892256
Indirubin,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	3055.7	Standard non polar	33892256
Indirubin,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)/C(=C2\C(=O)C3=CC=CC=C3N2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	3305.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Indirubin GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-0390000000-410947f1c15dc9a5efb0	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Indirubin 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indirubin 35V, Positive-QTOF	splash10-03xr-0090000000-5d7a5cde19caf82dc5c4	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Indirubin 35V, Negative-QTOF	splash10-03di-0090000000-32daf0ba3dd5126dd3c2	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 10V, Positive-QTOF	splash10-03di-0090000000-83721c94bd05c82ff63d	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 20V, Positive-QTOF	splash10-03dj-0490000000-8186d2ad41551d4a3030	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 40V, Positive-QTOF	splash10-001m-1960000000-b339ed52a626d0999bba	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 10V, Negative-QTOF	splash10-01q9-0950000000-d9ae18469cbb0465871c	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 20V, Negative-QTOF	splash10-03ec-4890000000-00c4aebd4b60b9143fca	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 40V, Negative-QTOF	splash10-001i-3490000000-0816fc1ba66f3b255fa0	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 10V, Negative-QTOF	splash10-03di-0090000000-fc429704171183f86ba8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 20V, Negative-QTOF	splash10-03di-0090000000-fc429704171183f86ba8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 40V, Negative-QTOF	splash10-001i-0690000000-8edeab68032a2ffd9cce	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 10V, Positive-QTOF	splash10-03di-0090000000-d2ff69a7f2ebf2ad3717	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 20V, Positive-QTOF	splash10-03di-0290000000-3e997be89ac4b2507ce6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indirubin 40V, Positive-QTOF	splash10-0w30-0690000000-f0409ce01d37892d3205	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB12379

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00026982

Chemspider ID

4514277

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Indirubin

METLIN ID

Not Available

PubChem Compound

5359405

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 ]
Zhang X, Song Y, Wu Y, Dong Y, Lai L, Zhang J, Lu B, Dai F, He L, Liu M, Yi Z: Indirubin inhibits tumor growth by antitumor angiogenesis via blocking VEGFR2-mediated JAK/STAT3 signaling in endothelial cell. Int J Cancer. 2011 Nov 15;129(10):2502-11. doi: 10.1002/ijc.25909. Epub 2011 Apr 7. [PubMed:21207415 ]
Suzuki H, Kaneko T, Mizokami Y, Narasaka T, Endo S, Matsui H, Yanaka A, Hirayama A, Hyodo I: Therapeutic efficacy of the Qing Dai in patients with intractable ulcerative colitis. World J Gastroenterol. 2013 May 7;19(17):2718-22. doi: 10.3748/wjg.v19.i17.2718. [PubMed:23674882 ]

Showing metabocard for Indirubin (HMDB0240743)

MOL for HMDB0240743 (Indirubin)

3D MOL for HMDB0240743 (Indirubin)

3D SDF for HMDB0240743 (Indirubin)

3D-SDF for HMDB0240743 (Indirubin)

PDB for HMDB0240743 (Indirubin)

3D PDB for HMDB0240743 (Indirubin)

SMILES for HMDB0240743 (Indirubin)

INCHI for HMDB0240743 (Indirubin)

Structure for HMDB0240743 (Indirubin)

3D Structure for HMDB0240743 (Indirubin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra