NP-MRD: Showing NP-Card for Indigo (NP0137146)

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Record Information

Version

2.0

Created at

2022-05-30 16:43:03 UTC

Updated at

2022-05-30 16:43:04 UTC

NP-MRD ID

NP0137146

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Indigo

Description

(E)-1H,1'H,3H,3'H-[2,2'-biindolylidene]-3,3'-dione belongs to the class of organic compounds known as indolines. Indigo is found in Couroupita guianensis, Indigofera suffruticosa, Indigofera truxillensis, Isatis tinctoria and Persicaria tinctoria. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole (E)-1H,1'H,3H,3'H-[2,2'-biindolylidene]-3,3'-dione is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 33  0  0  0  0  0  0  0  0999 V2000
    1.0198   -2.3074    0.7791 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4515   -1.1801    0.4563 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6373   -0.0480    0.0253 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6829    0.0336   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5794   -1.0247    0.1472 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8950   -0.5557   -0.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1241   -1.1990   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2918   -0.5347   -0.3271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2163    0.7968   -0.7456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0142    1.4623   -0.8551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8634    0.7409   -0.5263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4849    1.1675   -0.5444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0444    2.3065   -0.8702 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5565    1.0014   -0.2309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8888    0.5404    0.0303 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1232    1.1837   -0.0694 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2894    0.5133    0.2444 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2818   -0.8030    0.6639 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0508   -1.4167    0.7544 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8723   -0.7689    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2874   -1.9781    0.4765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1956   -2.2139    0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2521   -0.9963   -0.2620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1112    1.3561   -1.0007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9720    2.4952   -1.1811 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2643    1.9522   -0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1099    2.2210   -0.4016 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2393    1.0229    0.1631 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2004   -1.3200    0.9076 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0295   -2.4473    1.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  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
  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
 20  2  1  0
 12  4  1  0
 20 15  1  0
 11  6  1  0
 14 26  1  0
 16 27  1  0
 17 28  1  0
 18 29  1  0
 19 30  1  0
  5 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  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>
NP0137146

> <DATABASE_NAME>
NP-MRD

> <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

$$$$

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

View in JSmol

Synonyms

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

Chemical Formula

C₁₆H₁₀N₂O₂

Average Mass

262.2680 Da

Monoisotopic Mass

262.07423 Da

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Couroupita guianensis	LOTUS Database	35616633
Indigofera suffruticosa	LOTUS Database	35616633
Indigofera truxillensis	LOTUS Database	35616633
Isatis tinctoria	LOTUS Database	35616633
Persicaria tinctoria	LOTUS Database	35616633

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

Physical Properties

State

Not Available

Experimental 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

Predicted 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

5318432

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Indigo (NP0137146)

MOL for NP0137146 (Indigo)

3D MOL for NP0137146 (Indigo)

3D SDF for NP0137146 (Indigo)

3D-SDF for NP0137146 (Indigo)

PDB for NP0137146 (Indigo)

3D PDB for NP0137146 (Indigo)

SMILES for NP0137146 (Indigo)

INCHI for NP0137146 (Indigo)

Structure for NP0137146 (Indigo)

3D Structure for NP0137146 (Indigo)