NP-MRD: Showing NP-Card for codonopsine (NP0261301)

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Record Information

Version

2.0

Created at

2022-09-08 03:42:47 UTC

Updated at

2022-09-08 03:42:47 UTC

NP-MRD ID

NP0261301

Secondary Accession Numbers

None

Natural Product Identification

Common Name

codonopsine

Description

Codonopsine belongs to the class of organic compounds known as phenylpyrrolidines. These are polycyclic aromatic compounds containing a benzene ring linked to a pyrrolidine ring through a CC or CN bond. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. codonopsine is found in Codonopsis clematidea. codonopsine was first documented in 2008 (PMID: 18404331). Based on a literature review a small amount of articles have been published on Codonopsine (PMID: 30777662) (PMID: 24887531).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 41  0  0  0  0  0  0  0  0999 V2000
    5.2545    1.9005    0.0405 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5401    0.7019    0.2475 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1653    0.6684    0.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5096    1.8327   -0.2170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1436    1.7632   -0.3369 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4215    0.6043   -0.1398 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0275    0.6728   -0.2999 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6432    0.6456    1.0883 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0258    1.9084    1.5185 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8021   -0.3130    0.9994 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9221   -1.1218    2.1247 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5047   -1.1406   -0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8244   -1.4483   -0.8844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6058   -0.4073   -1.0477 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2307    0.1540   -2.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1192   -0.5336    0.1937 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4884   -0.5140    0.3254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1911   -1.6637    0.6622 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6025   -2.9059    0.8918 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0324    2.6648    0.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9567    2.3685   -0.9166 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3422    1.7098    0.0395 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0302    2.7780   -0.3846 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6336    2.7031   -0.6057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2961    1.6573   -0.7268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9411    0.2381    1.8455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6643    2.3294    0.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7390    0.2730    0.9089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4620   -0.7231    2.8429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0691   -2.1141    0.1157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3274   -2.3068   -0.3966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7294   -1.7118   -1.9548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5247   -0.5888   -0.8296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1412    0.7431   -1.9908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4913    0.8978   -2.6452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3915   -0.5868   -3.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5539   -1.4351    0.3467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3734   -3.6857    0.7548 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2121   -2.9453    1.9158 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7930   -3.0688    0.1516 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 17  3  1  0
 14  7  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  5 24  1  0
 16 37  1  0
 19 38  1  0
 19 39  1  0
 19 40  1  0
  7 25  1  6
  8 26  1  1
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  1
 13 31  1  0
 13 32  1  0
 13 33  1  0
 15 34  1  0
 15 35  1  0
 15 36  1  0
M  END


  Mrv1652309082205422D          

 19 20  0  0  1  0            999 V2000
   -0.0000    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.7661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1665    3.2361    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119    1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376    3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    5.9411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.7661    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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  0  0  0  0
  6 16  1  0  0  0  0
 16 17  2  0  0  0  0
  3 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0261301

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C=C1OC)[C@@H]1[C@@H](O)[C@H](O)[C@@H](C)N1C

> <INCHI_IDENTIFIER>
InChI=1S/C14H21NO4/c1-8-13(16)14(17)12(15(8)2)9-5-6-10(18-3)11(7-9)19-4/h5-8,12-14,16-17H,1-4H3/t8-,12-,13-,14-/m1/s1

> <INCHI_KEY>
WCNPJVPXLWJQIR-HKSFMPNISA-N

> <FORMULA>
C14H21NO4

> <MOLECULAR_WEIGHT>
267.325

> <EXACT_MASS>
267.14705816

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
28.93486697117128

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2-(3,4-dimethoxyphenyl)-1,5-dimethylpyrrolidine-3,4-diol

> <JCHEM_LOGP>
0.6434473190000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.638306017685014

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.209458603426278

> <JCHEM_PKA_STRONGEST_BASIC>
7.68309602639963

> <JCHEM_POLAR_SURFACE_AREA>
62.160000000000004

> <JCHEM_REFRACTIVITY>
71.5721

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
codonopsine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.000  13.400   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334  12.630   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  10.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   8.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   8.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.044   6.041   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.104   4.100   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       3.009   2.854   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.342   2.854   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.088   5.565   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -1.377   6.041   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   8.780   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.000  10.320   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334  11.090   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.334  12.630   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   16                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    7   15                                                  
CONECT   15   14                                                            
CONECT   16    6   17                                                       
CONECT   17   16    3   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₁NO₄

Average Mass

267.3250 Da

Monoisotopic Mass

267.14706 Da

IUPAC Name

(2R,3R,4R,5R)-2-(3,4-dimethoxyphenyl)-1,5-dimethylpyrrolidine-3,4-diol

Traditional Name

codonopsine

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C=C1OC)[C@@H]1[C@@H](O)[C@H](O)[C@@H](C)N1C

InChI Identifier

InChI=1S/C14H21NO4/c1-8-13(16)14(17)12(15(8)2)9-5-6-10(18-3)11(7-9)19-4/h5-8,12-14,16-17H,1-4H3/t8-,12-,13-,14-/m1/s1

InChI Key

WCNPJVPXLWJQIR-HKSFMPNISA-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
Codonopsis clematidea	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpyrrolidines. These are polycyclic aromatic compounds containing a benzene ring linked to a pyrrolidine ring through a CC or CN bond. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolidines

Sub Class

Phenylpyrrolidines

Direct Parent

Phenylpyrrolidines

Alternative Parents

Substituents

2-phenylpyrrolidine
O-dimethoxybenzene
Dimethoxybenzene
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
Alkyl aryl ether
Aralkylamine
Monocyclic benzene moiety
N-alkylpyrrolidine
Benzenoid
Pyrrole
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
1,2-diol
1,2-aminoalcohol
Azacycle
Ether
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Amine
Organic nitrogen compound
Organopnictogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrrolidines (CHEBI:3805 )

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	0.64	ChemAxon
pKa (Strongest Acidic)	13.21	ChemAxon
pKa (Strongest Basic)	7.68	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	62.16 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	71.57 m³·mol⁻¹	ChemAxon
Polarizability	28.93 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

C00002029

Chemspider ID

390995

KEGG Compound ID

C10137

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442631

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

El-Nezhawy AOH, Alrobaian M, Khames A, El-Badawy MF, Abdelwahab SF: Design and total synthesis of (-)-codonopsinine, (-)-codonopsine and codonopsinine analogues by O-(2-oxopyrrolidin-5-yl)trichloroacetimidate as amidoalkylating agent with improved antimicrobial activity via solid lipid nanoparticle formulations. Bioorg Med Chem. 2019 Apr 1;27(7):1263-1273. doi: 10.1016/j.bmc.2019.02.021. Epub 2019 Feb 13. [PubMed:30777662 ]
Dharuman S, Palanivel AK, Vankar YD: An easy route to synthetic analogues of radicamine B, codonopsine and codonopsinine from D-mannitol. Org Biomol Chem. 2014 Jul 21;12(27):4983-98. doi: 10.1039/c4ob00503a. [PubMed:24887531 ]
Ishida S, Okasaka M, Ramos F, Kashiwada Y, Takaishi Y, Kodzhimatov OK, Ashurmetov O: New alkaloid from the aerial parts of Codonopsis clematidea. J Nat Med. 2008 Apr;62(2):236-8. doi: 10.1007/s11418-007-0219-7. Epub 2008 Jan 11. [PubMed:18404331 ]
LOTUS database [Link]

Showing NP-Card for codonopsine (NP0261301)

MOL for NP0261301 (codonopsine)

3D MOL for NP0261301 (codonopsine)

3D SDF for NP0261301 (codonopsine)

3D-SDF for NP0261301 (codonopsine)

PDB for NP0261301 (codonopsine)

3D PDB for NP0261301 (codonopsine)

SMILES for NP0261301 (codonopsine)

INCHI for NP0261301 (codonopsine)

Structure for NP0261301 (codonopsine)

3D Structure for NP0261301 (codonopsine)