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Showing NP-Card for 2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile (NP0285379)

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Record Information
Version2.0
Created at2022-09-09 13:32:01 UTC
Updated at2022-09-09 13:32:01 UTC
NP-MRD IDNP0285379
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile
Description(+)-(R)-3-cyanomethyl-3-hydroxyoxindole 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. 2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile is found in Brassica oleracea and Pseudomonas cichorii. Based on a literature review very few articles have been published on (+)-(r)-3-cyanomethyl-3-hydroxyoxindole.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)


  Mrv1652309092215322D          

 14 15  0  0  1  0            999 V2000
    0.4243   -3.4279    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4243   -2.6029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4243   -1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4743   -2.1191    0.0000 O   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
   -0.1712   -0.6979    0.0000 O   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  2  3  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
  4 14  1  0  0  0  0
M  END
Download

3D MOL for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)

     RDKit          3D

 22 23  0  0  0  0  0  0  0  0999 V2000
   -2.2631   -1.7132   -1.6746 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0879   -1.3164   -0.6122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8418   -0.8075    0.7321 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8454    0.3128    0.7470 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7230    0.7240    2.0867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2244    1.4772   -0.0312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3832    2.2580    0.0113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796    1.7477   -0.8561 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8098    0.8297   -0.7356 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0265    0.7386   -1.4151 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8857   -0.2719   -1.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5700   -1.1755   -0.0863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3768   -1.0809    0.5754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4778   -0.0632    0.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7975   -0.4248    1.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4836   -1.6008    1.3969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5983    0.8527    2.5091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0640    2.1599   -0.7116 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2407    1.4733   -2.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8420   -0.3704   -1.5811 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2791   -1.9728    0.1661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0833   -1.7764    1.3644 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14  4  1  0
  4  5  1  1
  4  3  1  0
  3  2  1  0
  2  1  3  0
  4  6  1  0
 14  9  1  0
  7 18  1  0
 10 19  1  0
 11 20  1  0
 12 21  1  0
 13 22  1  0
  5 17  1  0
  3 15  1  0
  3 16  1  0
M  END
Download

3D SDF for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)


  Mrv1652309092215322D          

 14 15  0  0  1  0            999 V2000
    0.4243   -3.4279    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4243   -2.6029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4243   -1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4743   -2.1191    0.0000 O   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
   -0.1712   -0.6979    0.0000 O   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  2  3  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
  4 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0285379

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=NC2=CC=CC=C2[C@]1(O)CC#N

> <INCHI_IDENTIFIER>
InChI=1S/C10H8N2O2/c11-6-5-10(14)7-3-1-2-4-8(7)12-9(10)13/h1-4,14H,5H2,(H,12,13)/t10-/m1/s1

> <INCHI_KEY>
IXOBWMNTICTXOJ-SNVBAGLBSA-N

> <FORMULA>
C10H8N2O2

> <MOLECULAR_WEIGHT>
188.186

> <EXACT_MASS>
188.058577506

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
18.39464284647082

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(3R)-2,3-dihydroxy-3H-indol-3-yl]acetonitrile

> <JCHEM_LOGP>
0.9332512393333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.653275569446013

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.1649396926925215

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5705764162126011

> <JCHEM_POLAR_SURFACE_AREA>
76.61

> <JCHEM_REFRACTIVITY>
51.406200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-[(3R)-2,3-dihydroxyindol-3-yl]acetonitrile

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)

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PDB for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  N   UNK     0       0.792  -6.399   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.792  -4.859   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.792  -3.319   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.752  -3.956   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.320  -1.303   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6   14                                             
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9    4                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)
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SMILES for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)
OC1=NC2=CC=CC=C2[C@]1(O)CC#N
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INCHI for NP0285379 (2-[(3r)-2,3-dihydroxyindol-3-yl]acetonitrile)
InChI=1S/C10H8N2O2/c11-6-5-10(14)7-3-1-2-4-8(7)12-9(10)13/h1-4,14H,5H2,(H,12,13)/t10-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC10H8N2O2
Average Mass188.1860 Da
Monoisotopic Mass188.05858 Da
IUPAC Name2-[(3R)-2,3-dihydroxy-3H-indol-3-yl]acetonitrile
Traditional Name2-[(3R)-2,3-dihydroxyindol-3-yl]acetonitrile
CAS Registry NumberNot Available
SMILES
OC1=NC2=CC=CC=C2[C@]1(O)CC#N
InChI Identifier
InChI=1S/C10H8N2O2/c11-6-5-10(14)7-3-1-2-4-8(7)12-9(10)13/h1-4,14H,5H2,(H,12,13)/t10-/m1/s1
InChI KeyIXOBWMNTICTXOJ-SNVBAGLBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Brassica oleraceaLOTUS Database
Pseudomonas cichoriiLOTUS Database
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.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassIndolines  
Direct ParentIndolines  
Alternative Parents
Substituents
  • Dihydroindole
    • 

  • Benzenoid
    • 

  • Tertiary alcohol
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Secondary carboxylic acid amide
    • 

  • Carboxylic acid derivative
    • 

  • Carbonitrile
    • 

  • Azacycle
    • 

  • Nitrile
    • 

  • Alcohol
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Cyanide
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.93ChemAxon
pKa (Strongest Acidic)2.16ChemAxon
pKa (Strongest Basic)-0.57ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area76.61 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity51.41 m³·mol⁻¹ChemAxon
Polarizability18.39 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID75140297  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101797114  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]