NP-MRD: Showing NP-Card for (-)-Dianthin F (NP0072058)

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Record Information

Version

2.0

Created at

2022-04-28 17:26:22 UTC

Updated at

2022-04-28 17:26:22 UTC

NP-MRD ID

NP0072058

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Dianthin F

Description

(6S,9S,12S,17aS)-6,12-dibenzyl-1,4,7,10-tetrahydroxy-9-(propan-2-yl)-3H,6H,9H,12H,13H,15H,16H,17H,17aH-pyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecan-13-one 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 F is found in Dianthus longicalyx and Dianthus superbus var.longicalycinus (MAXIM.) WILL . Based on a literature review very few articles have been published on (6S,9S,12S,17aS)-6,12-dibenzyl-1,4,7,10-tetrahydroxy-9-(propan-2-yl)-3H,6H,9H,12H,13H,15H,16H,17H,17aH-pyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecan-13-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219262D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282219262D          

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    3.1060    0.0768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2935   -0.0663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0112   -0.8415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1988   -0.9847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6685   -0.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9508    0.4226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7633    0.5657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5671    1.6659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8256    2.0277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9406    2.8446    0.0000 C   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  1 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
 12 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 32 37  1  0  0  0  0
  9 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  8 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072058

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)CNC(=O)[C@@H]2CCCN2C(=O)[C@H](CC2=CC=CC=C2)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H37N5O5/c1-19(2)26-29(39)33-23(17-21-12-7-4-8-13-21)30(40)35-15-9-14-24(35)28(38)31-18-25(36)32-22(27(37)34-26)16-20-10-5-3-6-11-20/h3-8,10-13,19,22-24,26H,9,14-18H2,1-2H3,(H,31,38)(H,32,36)(H,33,39)(H,34,37)/t22-,23-,24-,26-/m0/s1

> <INCHI_KEY>
PDNKJYMGQZYDRS-IGRGDXOOSA-N

> <FORMULA>
C30H37N5O5

> <MOLECULAR_WEIGHT>
547.656

> <EXACT_MASS>
547.279469311

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
56.89907139660063

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S,9S,12S,17aS)-6,12-dibenzyl-9-(propan-2-yl)-hexadecahydro-1H-pyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecane-1,4,7,10,13-pentone

> <ALOGPS_LOGP>
1.76

> <JCHEM_LOGP>
1.221454305333334

> <ALOGPS_LOGS>
-3.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.19938826423876

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.685760273219868

> <JCHEM_PKA_STRONGEST_BASIC>
-3.401604330344545

> <JCHEM_POLAR_SURFACE_AREA>
136.71

> <JCHEM_REFRACTIVITY>
147.91579999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.48e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S,9S,12S,17aS)-6,12-dibenzyl-9-isopropyl-dodecahydropyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecane-1,4,7,10,13-pentone

> <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  N   UNK     0      10.483   6.084   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      10.058   7.564   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      11.128   8.672   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       8.564   7.937   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       7.494   6.829   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       5.955   6.883   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.232   8.243   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.139   5.577   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       5.862   4.217   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       5.335   2.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.818   2.503   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.325   1.591   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       7.841   1.858   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       9.055   0.910   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.840  -0.615   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.483   1.486   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.696   0.538   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.124   1.115   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.482  -0.987   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      10.697   3.011   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      11.974   3.872   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.358   3.197   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      11.867   5.408   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.144   6.270   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.528   5.594   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      15.804   6.455   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      17.189   5.780   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      17.296   4.244   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      16.019   3.383   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      14.635   4.058   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.798   0.143   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.281  -0.124   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.754  -1.571   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.238  -1.838   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.248  -0.658   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.775   0.789   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       3.291   1.056   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.792   3.110   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       3.408   3.785   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.622   5.310   0.000  0.00  0.00           C+0
CONECT    1    2   23                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   40                                                  
CONECT    9    8   10   38                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   16   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    1   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   25                                                       
CONECT   31   12   32                                                       
CONECT   32   31   33   37                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   32                                                       
CONECT   38    9   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39    8                                                       
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₇N₅O₅

Average Mass

547.6560 Da

Monoisotopic Mass

547.27947 Da

IUPAC Name

(6S,9S,12S,17aS)-6,12-dibenzyl-9-(propan-2-yl)-hexadecahydro-1H-pyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecane-1,4,7,10,13-pentone

Traditional Name

(6S,9S,12S,17aS)-6,12-dibenzyl-9-isopropyl-dodecahydropyrrolo[1,2-a]1,4,7,10,13-pentaazacyclopentadecane-1,4,7,10,13-pentone

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)CNC(=O)[C@@H]2CCCN2C(=O)[C@H](CC2=CC=CC=C2)NC1=O

InChI Identifier

InChI=1S/C30H37N5O5/c1-19(2)26-29(39)33-23(17-21-12-7-4-8-13-21)30(40)35-15-9-14-24(35)28(38)31-18-25(36)32-22(27(37)34-26)16-20-10-5-3-6-11-20/h3-8,10-13,19,22-24,26H,9,14-18H2,1-2H3,(H,31,38)(H,32,36)(H,33,39)(H,34,37)/t22-,23-,24-,26-/m0/s1

InChI Key

PDNKJYMGQZYDRS-IGRGDXOOSA-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 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
Pyrrolidine
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen 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	1.76	ALOGPS
logP	1.22	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	10.69	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	136.71 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	147.92 m³·mol⁻¹	ChemAxon
Polarizability	56.9 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

9424829

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11249796

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Dianthin F (NP0072058)

MOL for NP0072058 ((-)-Dianthin F)

3D MOL for NP0072058 ((-)-Dianthin F)

3D SDF for NP0072058 ((-)-Dianthin F)

3D-SDF for NP0072058 ((-)-Dianthin F)

PDB for NP0072058 ((-)-Dianthin F)

3D PDB for NP0072058 ((-)-Dianthin F)

SMILES for NP0072058 ((-)-Dianthin F)

INCHI for NP0072058 ((-)-Dianthin F)

Structure for NP0072058 ((-)-Dianthin F)

3D Structure for NP0072058 ((-)-Dianthin F)