NP-MRD: Showing NP-Card for verodoxin (NP0293921)

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Record Information

Version

2.0

Created at

2022-09-10 02:12:01 UTC

Updated at

2022-09-10 02:12:01 UTC

NP-MRD ID

NP0293921

Secondary Accession Numbers

None

Natural Product Identification

Common Name

verodoxin

Description

Verodoxin belongs to the class of organic compounds known as cardenolide glycosides and derivatives. Cardenolide glycosides and derivatives are compounds containing a carbohydrate glycosidically bound to the cardenolide moiety. verodoxin is found in Digitalis lanata. verodoxin was first documented in 2020 (PMID: 32035664). Based on a literature review very few articles have been published on Verodoxin (PMID: 35223908).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102204122D          

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M  END

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    4.3228   -0.7393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7875   -1.5084    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2939   -0.8571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0646   -0.0646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7474    0.3984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7742    1.2229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3987   -0.1080    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1184   -0.8839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168   -2.3009    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7927   -2.5812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4235   -2.0494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1994   -2.3297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3340   -2.7639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6826   -2.2576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4850   -3.0585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8705   -2.4028    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5902   -3.1787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7781   -3.3239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2463   -2.6932    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4342   -2.8384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6582   -3.7596    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1539   -3.6143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 22 27  1  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 28 32  1  0  0  0  0
 32 33  1  0  0  0  0
 19 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  0  0  0  0
 16 35  1  0  0  0  0
 35 36  1  6  0  0  0
 36 37  1  0  0  0  0
 38 37  1  6  0  0  0
 14 38  1  0  0  0  0
 38 39  1  0  0  0  0
 11 39  1  0  0  0  0
  9 40  1  0  0  0  0
  3 40  1  0  0  0  0
 40 41  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0293921

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1[C@@H](O)[C@@H](C)O[C@@H](O[C@H]2CC[C@@]3(C)[C@H](CC[C@@H]4[C@@H]3CC[C@]3(C)[C@H]([C@H](C[C@]43O)OC=O)C3=CC(=O)OC3)C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C31H46O10/c1-16-25(34)27(37-4)26(35)28(40-16)41-19-7-9-29(2)18(12-19)5-6-21-20(29)8-10-30(3)24(17-11-23(33)38-14-17)22(39-15-32)13-31(21,30)36/h11,15-16,18-22,24-28,34-36H,5-10,12-14H2,1-4H3/t16-,18-,19+,20+,21-,22+,24+,25+,26-,27+,28+,29+,30-,31+/m1/s1

> <INCHI_KEY>
XKWTVJAWBRFKLO-KZVRXWHRSA-N

> <FORMULA>
C31H46O10

> <MOLECULAR_WEIGHT>
578.699

> <EXACT_MASS>
578.309097681

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
62.412495999101765

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5S,7R,10R,11S,13S,14R,15R)-5-{[(2R,3R,4S,5S,6R)-3,5-dihydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-11-hydroxy-2,15-dimethyl-14-(5-oxo-2,5-dihydrofuran-3-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-13-yl formate

> <JCHEM_LOGP>
1.997423310999999

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.289362580441434

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.819603060987047

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2038803231861177

> <JCHEM_POLAR_SURFACE_AREA>
140.98000000000002

> <JCHEM_REFRACTIVITY>
145.47129999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5S,7R,10R,11S,13S,14R,15R)-5-{[(2R,3R,4S,5S,6R)-3,5-dihydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-11-hydroxy-2,15-dimethyl-14-(5-oxo-2H-furan-3-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-13-yl formate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.282 -11.092   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.759  -9.644   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.752  -8.466   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.268  -8.737   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.791 -10.186   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.261  -7.560   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.777  -7.831   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.737  -6.112   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.221  -5.841   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.698  -4.392   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.182  -4.121   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.341  -2.673   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.857  -2.402   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.850  -3.579   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.373  -2.131   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.366  -3.308   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.889  -1.859   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.405  -1.588   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.398  -2.766   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.069  -1.380   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.937  -2.816   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.882  -1.600   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.454  -0.121   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.728   0.744   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      10.779   2.283   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      11.944  -0.202   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      11.421  -1.650   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.365  -4.295   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.813  -4.818   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      11.990  -3.826   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      13.439  -4.349   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.090  -5.159   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.874  -4.214   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.505  -5.709   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       5.358  -4.485   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.835  -5.934   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       3.319  -6.205   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.326  -5.027   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.810  -5.298   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -1.229  -7.018   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       0.287  -6.747   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   40                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   40                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   39                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   38                                             
CONECT   15   14                                                            
CONECT   16   14   17   35                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21   33                                             
CONECT   20   19                                                            
CONECT   21   19   22   28                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   22                                                       
CONECT   28   21   29   32                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   28   33                                                       
CONECT   33   32   19   34   35                                             
CONECT   34   33                                                            
CONECT   35   33   16   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   14   39                                                  
CONECT   39   38   11                                                       
CONECT   40    9    3   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₁H₄₆O₁₀

Average Mass

578.6990 Da

Monoisotopic Mass

578.30910 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CO[C@H]1[C@@H](O)[C@@H](C)O[C@@H](O[C@H]2CC[C@@]3(C)[C@H](CC[C@@H]4[C@@H]3CC[C@]3(C)[C@H]([C@H](C[C@]43O)OC=O)C3=CC(=O)OC3)C2)[C@@H]1O

InChI Identifier

InChI=1S/C31H46O10/c1-16-25(34)27(37-4)26(35)28(40-16)41-19-7-9-29(2)18(12-19)5-6-21-20(29)8-10-30(3)24(17-11-23(33)38-14-17)22(39-15-32)13-31(21,30)36/h11,15-16,18-22,24-28,34-36H,5-10,12-14H2,1-4H3/t16-,18-,19+,20+,21-,22+,24+,25+,26-,27+,28+,29+,30-,31+/m1/s1

InChI Key

XKWTVJAWBRFKLO-KZVRXWHRSA-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
Digitalis lanata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cardenolide glycosides and derivatives. Cardenolide glycosides and derivatives are compounds containing a carbohydrate glycosidically bound to the cardenolide moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Cardenolide glycosides and derivatives

Alternative Parents

Substituents

Cardanolide-glycoside
Steroidal glycoside
Steroid ester
14-hydroxysteroid
Hydroxysteroid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
2-furanone
Dicarboxylic acid or derivatives
Monosaccharide
Oxane
Tertiary alcohol
Cyclic alcohol
Dihydrofuran
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Lactone
Oxacycle
Carboxylic acid derivative
Dialkyl ether
Organoheterocyclic compound
Acetal
Ether
Organic oxygen compound
Alcohol
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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

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

32700439

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

76960910

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ravi BG, Guardian MGE, Dickman R, Wang ZQ: Profiling and structural analysis of cardenolides in two species of Digitalis using liquid chromatography coupled with high-resolution mass spectrometry. J Chromatogr A. 2020 May 10;1618:460903. doi: 10.1016/j.chroma.2020.460903. Epub 2020 Jan 22. [PubMed:32035664 ]
Ma T, Wang H, Su T, Wang S: Case Report: Chronic Lymphocytic Leukemia With Recurrent Complement-Mediated Thrombotic Microangiopathy and C3 Glomerulonephritis. Front Med (Lausanne). 2022 Feb 10;9:813439. doi: 10.3389/fmed.2022.813439. eCollection 2022. [PubMed:35223908 ]
LOTUS database [Link]

Showing NP-Card for verodoxin (NP0293921)

MOL for NP0293921 (verodoxin)

3D MOL for NP0293921 (verodoxin)

3D SDF for NP0293921 (verodoxin)

3D-SDF for NP0293921 (verodoxin)

PDB for NP0293921 (verodoxin)

3D PDB for NP0293921 (verodoxin)

SMILES for NP0293921 (verodoxin)

INCHI for NP0293921 (verodoxin)

Structure for NP0293921 (verodoxin)

3D Structure for NP0293921 (verodoxin)