NP-MRD: Showing NP-Card for (3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol (NP0320454)

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Record Information

Version

2.0

Created at

2022-09-11 22:06:43 UTC

Updated at

2022-09-11 22:06:44 UTC

NP-MRD ID

NP0320454

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol

Description

Convolutamydine B 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. (3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol is found in Amathia convoluta. (3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol was first documented in 2006 (PMID: 16468740). Based on a literature review very few articles have been published on Convolutamydine B (PMID: 19504525).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122200062D          

 16 17  0  0  1  0            999 V2000
   -0.1712   -0.6979    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
    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
    4.0668    0.1271    0.0000 Br  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
    2.6378   -2.3479    0.0000 Br  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  1  0  0  0  0  0  0  0  0  0
    1.3018   -2.1741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5314   -1.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2558   -1.6771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8631   -2.2355    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0320454

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H8Br2ClNO2/c11-5-3-6(12)8-7(4-5)14-9(15)10(8,16)1-2-13/h3-4,16H,1-2H2,(H,14,15)/t10-/m1/s1

> <INCHI_KEY>
ZRDJKQFIKGOBIS-SNVBAGLBSA-N

> <FORMULA>
C10H8Br2ClNO2

> <MOLECULAR_WEIGHT>
369.44

> <EXACT_MASS>
366.861032

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
27.618565873716285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-4,6-dibromo-3-(2-chloroethyl)-3H-indole-2,3-diol

> <JCHEM_LOGP>
3.4222611616666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.030216440374303

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.652184751485367

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6524869973047817

> <JCHEM_POLAR_SURFACE_AREA>
52.82000000000001

> <JCHEM_REFRACTIVITY>
71.0972

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.320  -1.303   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    7 Br   UNK     0       7.591   0.237   0.000  0.00  0.00          Br+0
HETATM    8  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   10 Br   UNK     0       4.924  -4.383   0.000  0.00  0.00          Br+0
HETATM   11  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.430  -4.058   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.992  -3.591   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.478  -3.131   0.000  0.00  0.00           C+0
HETATM   16 Cl   UNK     0      -1.611  -4.173   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4   12                                                  
CONECT   12   11    2   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₈Br₂ClNO₂

Average Mass

369.4400 Da

Monoisotopic Mass

366.86103 Da

IUPAC Name

(3R)-4,6-dibromo-3-(2-chloroethyl)-3H-indole-2,3-diol

Traditional Name

(3R)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol

CAS Registry Number

Not Available

SMILES

OC1=NC2=CC(Br)=CC(Br)=C2[C@]1(O)CCCl

InChI Identifier

InChI=1S/C10H8Br2ClNO2/c11-5-3-6(12)8-7(4-5)14-9(15)10(8,16)1-2-13/h3-4,16H,1-2H2,(H,14,15)/t10-/m1/s1

InChI Key

ZRDJKQFIKGOBIS-SNVBAGLBSA-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
Amathia convoluta	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 bromide
Aryl halide
Benzenoid
Tertiary alcohol
Carboxamide group
Secondary carboxylic acid amide
Lactam
Carboxylic acid derivative
Azacycle
Alcohol
Organonitrogen compound
Organochloride
Organobromide
Organohalogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Alkyl halide
Alkyl chloride
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	3.42	ChemAxon
pKa (Strongest Acidic)	1.65	ChemAxon
pKa (Strongest Basic)	-0.65	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	52.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.1 m³·mol⁻¹	ChemAxon
Polarizability	27.62 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

557619

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

642417

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hara N, Nakamura S, Shibata N, Toru T: First enantioselective synthesis of (R)-convolutamydine B and E with N-(heteroarenesulfonyl)prolinamides. Chemistry. 2009 Jul 13;15(28):6790-3. doi: 10.1002/chem.200900944. [PubMed:19504525 ]
Nakamura T, Shirokawa S, Hosokawa S, Nakazaki A, Kobayashi S: Enantioselective total synthesis of convolutamydines B and E. Org Lett. 2006 Feb 16;8(4):677-9. doi: 10.1021/ol052871p. [PubMed:16468740 ]
LOTUS database [Link]

Showing NP-Card for (3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol (NP0320454)

MOL for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

3D MOL for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

3D SDF for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

3D-SDF for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

PDB for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

3D PDB for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

SMILES for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

INCHI for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

Structure for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)

3D Structure for NP0320454 ((3r)-4,6-dibromo-3-(2-chloroethyl)indole-2,3-diol)