NP-MRD: Showing NP-Card for Coscinoderine F (NP0331850)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2023-09-26 20:15:22 UTC

Updated at

2024-09-03 04:17:12 UTC

NP-MRD ID

NP0331850

Natural Product DOI

https://doi.org/10.57994/0956

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Coscinoderine F

Description

Coscinoderine F belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. Based on a literature review very few articles have been published on Coscinoderine F.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 09262320152D          

 31 32  0  0  1  0            999 V2000
    5.9149   -2.6755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1698   -3.4601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6178   -4.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8108   -3.9017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2588   -4.5148    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7068   -3.9017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9617   -3.1171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8998   -4.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9262   -4.9997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6713   -5.7843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8463   -5.7843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5914   -4.9997    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8067   -4.7448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9768   -3.6317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5288   -3.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3358   -3.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8879   -2.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6948   -2.7485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2469   -2.1354    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.9919   -1.3508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1849   -1.1793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6329   -1.7924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9300   -0.3947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0538   -2.3070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3088   -3.0916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1157   -3.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3707   -4.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1777   -4.2193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8186   -4.6608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7567   -3.7047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9498   -3.5332    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  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  1  0  0  0
  2 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 19 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 25 30  1  0  0  0  0
 30 31  2  0  0  0  0
 18 31  1  0  0  0  0
M  CHG  1  19   1
M  END


  Mrv2104 09262320152D          

 31 32  0  0  1  0            999 V2000
    5.9149   -2.6755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1698   -3.4601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6178   -4.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8108   -3.9017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2588   -4.5148    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7068   -3.9017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9617   -3.1171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8998   -4.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9262   -4.9997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6713   -5.7843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8463   -5.7843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5914   -4.9997    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8067   -4.7448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9768   -3.6317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5288   -3.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3358   -3.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8879   -2.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6948   -2.7485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2469   -2.1354    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.9919   -1.3508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1849   -1.1793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6329   -1.7924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9300   -0.3947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0538   -2.3070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3088   -3.0916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1157   -3.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3707   -4.0477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1777   -4.2193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8186   -4.6608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7567   -3.7047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9498   -3.5332    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  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  1  0  0  0
  2 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 19 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 25 30  1  0  0  0  0
 30 31  2  0  0  0  0
 18 31  1  0  0  0  0
M  CHG  1  19   1
M  END
> <DATABASE_ID>
NP0331850

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CCC[C@]1(CC\C(C)=C\CCCC1=[N+](CC(O)=O)C=C(CC(O)=O)C=C1)C(C)=C

> <INCHI_IDENTIFIER>
InChI=1S/C26H37NO4/c1-19(2)26(14-7-9-21(26)4)15-13-20(3)8-5-6-10-23-12-11-22(16-24(28)29)17-27(23)18-25(30)31/h8,11-12,17,21H,1,5-7,9-10,13-16,18H2,2-4H3,(H-,28,29,30,31)/p+1/b20-8+/t21-,26+/m1/s1

> <INCHI_KEY>
KTMCJRZISHIIAU-UBFXPIDCSA-O

> <FORMULA>
C26H38NO4

> <MOLECULAR_WEIGHT>
428.592

> <EXACT_MASS>
428.279535128

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
49.84793501333783

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,5-bis(carboxymethyl)-2-[(4E)-5-methyl-7-[(1R,2R)-2-methyl-1-(prop-1-en-2-yl)cyclopentyl]hept-4-en-1-yl]pyridin-1-ium

> <JCHEM_LOGP>
0.9708524011949202

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.5828464831215867

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5936768950771203

> <JCHEM_POLAR_SURFACE_AREA>
78.47999999999999

> <JCHEM_REFRACTIVITY>
124.42139999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1,5-bis(carboxymethyl)-2-[(4E)-5-methyl-7-[(1R,2R)-2-methyl-1-(prop-1-en-2-yl)cyclopentyl]hept-4-en-1-yl]pyridin-1-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-SEP-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-SEP-23         0                                  
HETATM    1  C   UNK     0      11.041  -4.994   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.517  -6.459   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.487  -7.603   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.980  -7.283   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.950  -8.428   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.919  -7.283   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.395  -5.819   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.413  -7.603   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.196  -9.333   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.720 -10.797   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.180 -10.797   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.704  -9.333   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.239  -8.857   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.023  -6.779   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.054  -5.635   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.560  -5.955   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.591  -4.810   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      18.097  -5.131   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      19.127  -3.986   0.000  0.00  0.00           N+1
HETATM   20  C   UNK     0      18.652  -2.522   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.145  -2.201   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      16.115  -3.346   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      16.669  -0.737   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      20.634  -4.306   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      21.110  -5.771   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      22.616  -6.091   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      23.092  -7.556   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      24.598  -7.876   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      22.061  -8.700   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      20.079  -6.915   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      18.573  -6.595   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    9   12                                             
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    5   13                                                  
CONECT   13   12                                                            
CONECT   14    2   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   31                                                  
CONECT   19   18   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   19   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   25   31                                                       
CONECT   31   30   18                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₈NO₄

Average Mass

428.5920 Da

Monoisotopic Mass

428.27954 Da

IUPAC Name

1,5-bis(carboxymethyl)-2-[(4E)-5-methyl-7-[(1R,2R)-2-methyl-1-(prop-1-en-2-yl)cyclopentyl]hept-4-en-1-yl]pyridin-1-ium

Traditional Name

1,5-bis(carboxymethyl)-2-[(4E)-5-methyl-7-[(1R,2R)-2-methyl-1-(prop-1-en-2-yl)cyclopentyl]hept-4-en-1-yl]pyridin-1-ium

CAS Registry Number

Not Available

SMILES

C[C@@H]1CCC[C@]1(CC\C(C)=C\CCCC1=[N+](CC(O)=O)C=C(CC(O)=O)C=C1)C(C)=C

InChI Identifier

InChI=1S/C26H37NO4/c1-19(2)26(14-7-9-21(26)4)15-13-20(3)8-5-6-10-23-12-11-22(16-24(28)29)17-27(23)18-25(30)31/h8,11-12,17,21H,1,5-7,9-10,13-16,18H2,2-4H3,(H-,28,29,30,31)/p+1/b20-8+/t21-,26+/m1/s1

InChI Key

KTMCJRZISHIIAU-UBFXPIDCSA-O

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	hnktran@kiost.ac.kr	Not Available	Not Available	2023-09-26	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	hnktran@kiost.ac.kr	Not Available	Not Available	2023-09-26	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Monocyclic monoterpenoid
11-noriridane monoterpenoid
Aromatic monoterpenoid
Alpha-amino acid or derivatives
Alpha-amino acid
Polyhalopyridine
2-halopyridine
Methylpyridine
Hydroxypyridine
Heterocyclic fatty acid
Branched fatty acid
Fatty acyl
Pyridine
Dicarboxylic acid or derivatives
Heteroaromatic compound
Secondary ketimine
Azacycle
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	0.97	ChemAxon
pKa (Strongest Acidic)	2.59	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	78.48 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	124.42 m³·mol⁻¹	ChemAxon
Polarizability	49.85 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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1021/acs.jnatprod.3c00358

Showing NP-Card for Coscinoderine F (NP0331850)

MOL for NP0331850 (Coscinoderine F)

3D MOL for NP0331850 (Coscinoderine F)

3D SDF for NP0331850 (Coscinoderine F)

3D-SDF for NP0331850 (Coscinoderine F)

PDB for NP0331850 (Coscinoderine F)

3D PDB for NP0331850 (Coscinoderine F)

SMILES for NP0331850 (Coscinoderine F)

INCHI for NP0331850 (Coscinoderine F)

Structure for NP0331850 (Coscinoderine F)

3D Structure for NP0331850 (Coscinoderine F)