NP-MRD: Showing NP-Card for (-)-Dianthin E (NP0072057)

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Record Information

Version

2.0

Created at

2022-04-28 17:26:16 UTC

Updated at

2022-04-28 17:26:16 UTC

NP-MRD ID

NP0072057

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Dianthin E

Description

Dianthin E belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. (-)-Dianthin E is found in Dianthus longicalyx, Dianthus superbus and Dianthus superbus var.longicalycinus (MAXIM.) WILL . (-)-Dianthin E was first documented in 2012 (PMID: 22325941). Based on a literature review a small amount of articles have been published on Dianthin E (PMID: 31614697).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219262D          

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M  END

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  Mrv1652304282219262D          

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    6.1452   -2.9790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7557   -3.7062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9698   -2.9527    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.3593   -2.2255    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1839   -2.1992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6189   -2.9001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4048   -3.6537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2294   -3.6274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4960   -3.0316    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9311   -3.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5415   -4.4598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6714   -3.0578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3078   -1.5065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5438   -1.1951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6039   -0.3723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4824    1.3845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0473    2.0855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3070    1.4108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3980   -1.4456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8330   -2.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6576   -2.1203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0927   -2.8213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7031   -3.5485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8786   -3.5748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4435   -2.8739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  1 23  1  0  0  0  0
 23 24  2  0  0  0  0
 21 25  1  1  0  0  0
 25 26  1  0  0  0  0
 17 27  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 27 30  1  6  0  0  0
 14 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 13 33  1  0  0  0  0
  5 34  1  1  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
  1 37  1  1  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 41 42  1  0  0  0  0
 42 43  2  0  0  0  0
 38 43  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072057

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)[C@@H]1NC(=O)[C@H](CO)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@@H](NC(=O)CNC(=O)[C@@H]2CCCN2C1=O)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H44N6O7/c1-5-18(4)25-30(43)36-13-9-12-22(36)28(41)31-15-23(38)34-24(17(2)3)29(42)32-20(14-19-10-7-6-8-11-19)26(39)33-21(16-37)27(40)35-25/h6-8,10-11,17-18,20-22,24-25,37H,5,9,12-16H2,1-4H3,(H,31,41)(H,32,42)(H,33,39)(H,34,38)(H,35,40)/t18-,20-,21-,22-,24-,25-/m0/s1

> <INCHI_KEY>
NHNDCMROOPKDNF-BYZHJWIBSA-N

> <FORMULA>
C30H44N6O7

> <MOLECULAR_WEIGHT>
600.717

> <EXACT_MASS>
600.327147781

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
61.968278951922045

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S,9S,12S,15S,20aS)-9-benzyl-15-[(2S)-butan-2-yl]-12-(hydroxymethyl)-6-(propan-2-yl)-icosahydropyrrolo[1,2-a]1,4,7,10,13,16-hexaazacyclooctadecane-1,4,7,10,13,16-hexone

> <ALOGPS_LOGP>
0.50

> <JCHEM_LOGP>
-0.6862371400000006

> <ALOGPS_LOGS>
-3.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.85834726361509

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.387646309431108

> <JCHEM_PKA_STRONGEST_BASIC>
-2.84439959199352

> <JCHEM_POLAR_SURFACE_AREA>
186.04

> <JCHEM_REFRACTIVITY>
155.73449999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.60e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S,9S,12S,15S,20aS)-9-benzyl-15-[(2S)-butan-2-yl]-12-(hydroxymethyl)-6-isopropyl-tetradecahydropyrrolo[1,2-a]1,4,7,10,13,16-hexaazacyclooctadecane-1,4,7,10,13,16-hexone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      16.004  -2.748   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      15.192  -1.439   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      15.919  -0.082   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      17.458  -0.033   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      15.107   1.227   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      13.567   1.178   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      12.755   2.486   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      13.482   3.844   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.216   2.437   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      10.489   1.080   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       8.950   1.031   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.138   2.339   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.223  -0.327   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       9.035  -1.635   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       8.520  -3.043   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.768  -3.042   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       9.120  -4.301   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      10.659  -4.252   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      11.471  -5.561   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.744  -6.918   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.010  -5.512   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      13.737  -4.154   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      15.277  -4.105   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      16.089  -5.414   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      13.822  -6.820   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      15.362  -6.771   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.393  -5.659   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.205  -6.967   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.478  -8.325   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.853  -5.708   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.041  -2.812   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.615  -2.231   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.727  -0.695   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      15.834   2.584   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      15.022   3.893   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      17.373   2.633   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      17.543  -2.699   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      18.355  -4.007   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      19.894  -3.958   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      20.706  -5.266   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      19.979  -6.624   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      18.440  -6.673   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      17.628  -5.365   0.000  0.00  0.00           C+0
CONECT    1    2   23   37                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   33                                                  
CONECT   14   13   15   31                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   27                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22    1   24                                                  
CONECT   24   23                                                            
CONECT   25   21   26                                                       
CONECT   26   25                                                            
CONECT   27   17   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27                                                            
CONECT   31   14   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   13                                                       
CONECT   34    5   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37    1   38                                                       
CONECT   38   37   39   43                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   38                                                       
MASTER        0    0    0    0    0    0    0    0   43    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₄N₆O₇

Average Mass

600.7170 Da

Monoisotopic Mass

600.32715 Da

IUPAC Name

(6S,9S,12S,15S,20aS)-9-benzyl-15-[(2S)-butan-2-yl]-12-(hydroxymethyl)-6-(propan-2-yl)-icosahydropyrrolo[1,2-a]1,4,7,10,13,16-hexaazacyclooctadecane-1,4,7,10,13,16-hexone

Traditional Name

(6S,9S,12S,15S,20aS)-9-benzyl-15-[(2S)-butan-2-yl]-12-(hydroxymethyl)-6-isopropyl-tetradecahydropyrrolo[1,2-a]1,4,7,10,13,16-hexaazacyclooctadecane-1,4,7,10,13,16-hexone

CAS Registry Number

Not Available

SMILES

CC[C@H](C)[C@@H]1NC(=O)[C@H](CO)NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@@H](NC(=O)CNC(=O)[C@@H]2CCCN2C1=O)C(C)C

InChI Identifier

InChI=1S/C30H44N6O7/c1-5-18(4)25-30(43)36-13-9-12-22(36)28(41)31-15-23(38)34-24(17(2)3)29(42)32-20(14-19-10-7-6-8-11-19)26(39)33-21(16-37)27(40)35-25/h6-8,10-11,17-18,20-22,24-25,37H,5,9,12-16H2,1-4H3,(H,31,41)(H,32,42)(H,33,39)(H,34,38)(H,35,40)/t18-,20-,21-,22-,24-,25-/m0/s1

InChI Key

NHNDCMROOPKDNF-BYZHJWIBSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Dianthus longicalyx	LOTUS Database	35616633
Dianthus superbus	LOTUS Database	35616633
Dianthus superbus var.longicalycinus (MAXIM.) WILL	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Cyclic alpha peptide
Macrolactam
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Benzenoid
Tertiary carboxylic acid amide
Pyrrolidine
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Primary alcohol
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	0.5	ALOGPS
logP	-0.69	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	10.39	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	186.04 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	155.73 m³·mol⁻¹	ChemAxon
Polarizability	61.97 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00031738

Chemspider ID

10208560

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21589729

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Fuchs H: Dianthin and Its Potential in Targeted Tumor Therapies. Toxins (Basel). 2019 Oct 11;11(10). pii: toxins11100592. doi: 10.3390/toxins11100592. [PubMed:31614697 ]
Tong Y, Luo JG, Wang R, Wang XB, Kong LY: New cyclic peptides with osteoblastic proliferative activity from Dianthus superbus. Bioorg Med Chem Lett. 2012 Mar 1;22(5):1908-11. doi: 10.1016/j.bmcl.2012.01.058. Epub 2012 Jan 28. [PubMed:22325941 ]

Showing NP-Card for (-)-Dianthin E (NP0072057)

MOL for NP0072057 ((-)-Dianthin E)

3D MOL for NP0072057 ((-)-Dianthin E)

3D SDF for NP0072057 ((-)-Dianthin E)

3D-SDF for NP0072057 ((-)-Dianthin E)

PDB for NP0072057 ((-)-Dianthin E)

3D PDB for NP0072057 ((-)-Dianthin E)

SMILES for NP0072057 ((-)-Dianthin E)

INCHI for NP0072057 ((-)-Dianthin E)

Structure for NP0072057 ((-)-Dianthin E)

3D Structure for NP0072057 ((-)-Dianthin E)