NP-MRD: Showing NP-Card for (+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile (NP0036798)

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Record Information

Version

2.0

Created at

2021-06-20 19:52:37 UTC

Updated at

2021-06-30 00:08:39 UTC

NP-MRD ID

NP0036798

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile

Provided By

JEOL Database JEOL Logo

Description

CHEMBL2063285 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. (+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile is found in Isatis indigotica. (+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile was first documented in 2012 (Chen, M., et al.). Based on a literature review very few articles have been published on CHEMBL2063285.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202121523D          

 23 24  0  0  0  0            999 V2000
   -1.2189   -4.2800    3.2855 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6512   -4.4170    2.2833 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0545   -4.5979    1.0093 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5370   -3.7686   -0.1345 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1997   -4.0233   -1.3303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0623   -4.0593   -0.2887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5511   -5.1292   -0.6142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7424   -2.8785   -0.0219 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8579   -1.8337    0.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1702   -0.5191    0.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1056    0.3719    0.6558 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2260   -0.0625    0.5189 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5028   -1.3936    0.2210 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7916   -1.7767    0.0225 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5415   -2.2850    0.1032 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1160   -4.3528    1.1403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0331   -5.6603    0.7342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1922   -4.8276   -1.7251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7495   -2.8025   -0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1961   -0.1802    0.5764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3055    1.4172    0.8816 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0417    0.6481    0.6285 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7745   -2.5176   -0.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0  0  0  0
  4 15  1  0  0  0  0
 15 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 12  1  0  0  0  0
  4  5  1  6  0  0  0
 15  9  1  0  0  0  0
  4  3  1  0  0  0  0
  3  2  1  0  0  0  0
 11 10  1  0  0  0  0
  2  1  3  0  0  0  0
 10  9  2  0  0  0  0
  8  6  1  0  0  0  0
  6  4  1  0  0  0  0
 12 11  2  0  0  0  0
  6  7  2  0  0  0  0
 12 22  1  0  0  0  0
 11 21  1  0  0  0  0
 10 20  1  0  0  0  0
  8 19  1  0  0  0  0
 14 23  1  0  0  0  0
  5 18  1  0  0  0  0
  3 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0036798

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2C(N([H])C(=O)[C@]2(O[H])C([H])([H])C#N)=C([H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C10H8N2O3/c11-5-4-10(15)8-6(12-9(10)14)2-1-3-7(8)13/h1-3,13,15H,4H2,(H,12,14)/t10-/m0/s1

> <INCHI_KEY>
MAPBAOFPTURBNK-JTQLQIEISA-N

> <FORMULA>
C10H8N2O3

> <MOLECULAR_WEIGHT>
204.185

> <EXACT_MASS>
204.053492126

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.893395525552805

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(3S)-3,4-dihydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]acetonitrile

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
-0.09777075266666681

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.335209767629639

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.45842246763857

> <JCHEM_PKA_STRONGEST_BASIC>
-4.495002413221674

> <JCHEM_POLAR_SURFACE_AREA>
93.35

> <JCHEM_REFRACTIVITY>
52.63200000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.60e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(3S)-3,4-dihydroxy-2-oxo-1H-indol-3-yl]acetonitrile

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  N   UNK     0      -1.219  -4.280   3.285  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.651  -4.417   2.283  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.055  -4.598   1.009  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.537  -3.769  -0.135  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.200  -4.023  -1.330  0.00  0.00           O+0
HETATM    6  C   UNK     0      -2.062  -4.059  -0.289  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.551  -5.129  -0.614  0.00  0.00           O+0
HETATM    8  N   UNK     0      -2.742  -2.878  -0.022  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.858  -1.834   0.211  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.170  -0.519   0.488  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.106   0.372   0.656  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.226  -0.063   0.519  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.503  -1.394   0.221  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.792  -1.777   0.023  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.542  -2.285   0.103  0.00  0.00           C+0
HETATM   16  H   UNK     0       1.116  -4.353   1.140  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.033  -5.660   0.734  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.192  -4.828  -1.725  0.00  0.00           H+0
HETATM   19  H   UNK     0      -3.749  -2.803  -0.035  0.00  0.00           H+0
HETATM   20  H   UNK     0      -3.196  -0.180   0.576  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.306   1.417   0.882  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.042   0.648   0.629  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.775  -2.518  -0.616  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    3    1                                                       
CONECT    3    4    2   16   17                                             
CONECT    4   15    5    3    6                                             
CONECT    5    4   18                                                       
CONECT    6    8    4    7                                                  
CONECT    7    6                                                            
CONECT    8    9    6   19                                                  
CONECT    9    8   15   10                                                  
CONECT   10   11    9   20                                                  
CONECT   11   10   12   21                                                  
CONECT   12   13   11   22                                                  
CONECT   13   15   14   12                                                  
CONECT   14   13   23                                                       
CONECT   15    4   13    9                                                  
CONECT   16    3                                                            
CONECT   17    3                                                            
CONECT   18    5                                                            
CONECT   19    8                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   14                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₈N₂O₃

Average Mass

204.1850 Da

Monoisotopic Mass

204.05349 Da

IUPAC Name

2-[(3S)-3,4-dihydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]acetonitrile

Traditional Name

2-[(3S)-3,4-dihydroxy-2-oxo-1H-indol-3-yl]acetonitrile

CAS Registry Number

Not Available

SMILES

[H]OC1=C2C(N([H])C(=O)[C@]2(O[H])C([H])([H])C#N)=C([H])C([H])=C1[H]

InChI Identifier

InChI=1S/C10H8N2O3/c11-5-4-10(15)8-6(12-9(10)14)2-1-3-7(8)13/h1-3,13,15H,4H2,(H,12,14)/t10-/m0/s1

InChI Key

MAPBAOFPTURBNK-JTQLQIEISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Isatis tinctoria	JEOL database	Chen, M., et al, J. Nat. Prod. 75, 1167 (2012)

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
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Tertiary alcohol
Carboxamide group
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Carbonitrile
Nitrile
Azacycle
Organonitrogen compound
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Carbonyl group
Organooxygen compound
Alcohol
Hydrocarbon derivative
Cyanide
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	0.36	ALOGPS
logP	-0.098	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	9.46	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	93.35 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	52.63 m³·mol⁻¹	ChemAxon
Polarizability	18.89 Å³	ChemAxon
Number of Rings	2	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

28516064

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

60156057

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chen, M., et al. (2012). Chen, M., et al, J. Nat. Prod. 75, 1167 (2012). J. Nat. Prod..

Showing NP-Card for (+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile (NP0036798)

MOL for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

3D MOL for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

3D SDF for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

3D-SDF for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

PDB for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

3D PDB for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

SMILES for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

INCHI for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

Structure for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)

3D Structure for NP0036798 ((+)-(S)-2-(3,4-dihydroxy-2-oxoindolin-3-yl)acetonitrile)