NP-MRD: Showing NP-Card for Rhodexin A (NP0052154)

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Record Information

Version

2.0

Created at

2022-04-27 23:18:51 UTC

Updated at

2022-04-27 23:18:52 UTC

NP-MRD ID

NP0052154

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rhodexin A

Description

4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-14-yl]-2,5-dihydrofuran-2-one 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. Rhodexin A is found in Convallaria keiskei, Dipcadi glaucum, Ornithogalum arcuatum, Rohdea japonica and Speirantha convallarioides. Based on a literature review very few articles have been published on 4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-14-yl]-2,5-dihydrofuran-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201182D          

 38 43  0  0  1  0            999 V2000
    4.2475    2.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0914    1.8134    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5596    1.1827    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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 30 38  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282201182D          

 38 43  0  0  1  0            999 V2000
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    0.1073    2.8462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9451    0.5269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6232    2.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3399    1.2325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6202    0.4566    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4323    0.3114    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7126   -0.4646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1808   -1.0953    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3687   -0.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0884   -0.1741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8369   -1.5808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4611   -1.8712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5247   -0.6098    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9641    0.9421    0.0000 O   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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  7  5  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  1  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 11 18  1  0  0  0  0
 16 19  1  6  0  0  0
 19 20  2  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
 23 24  1  0  0  0  0
 19 24  1  0  0  0  0
 12 25  1  6  0  0  0
 11 26  1  6  0  0  0
  5 27  1  6  0  0  0
  2 28  1  6  0  0  0
 29 28  1  6  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 29 34  1  0  0  0  0
 33 35  1  6  0  0  0
 32 36  1  1  0  0  0
 31 37  1  1  0  0  0
 30 38  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0052154

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C29H44O9/c1-14-23(32)24(33)25(34)26(37-14)38-17-6-8-27(2)16(11-17)4-5-19-22(27)20(30)12-28(3)18(7-9-29(19,28)35)15-10-21(31)36-13-15/h10,14,16-20,22-26,30,32-35H,4-9,11-13H2,1-3H3/t14-,16+,17-,18+,19+,20+,22+,23-,24-,25+,26+,27-,28+,29-/m0/s1

> <INCHI_KEY>
HFMLTKBZNAPPNY-GITSYYNXSA-N

> <FORMULA>
C29H44O9

> <MOLECULAR_WEIGHT>
536.662

> <EXACT_MASS>
536.298532997

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
57.30251425103777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2,5-dihydrofuran-2-one

> <ALOGPS_LOGP>
0.62

> <JCHEM_LOGP>
1.0346641110000014

> <ALOGPS_LOGS>
-3.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.218445752037837

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.181446972867483

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8443196870610494

> <JCHEM_POLAR_SURFACE_AREA>
145.91000000000003

> <JCHEM_REFRACTIVITY>
136.1027

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-5H-furan-2-one

> <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       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.374   6.011   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.151   5.043   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.675   6.491   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -5.154   6.919   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.459   7.436   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.184   6.572   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.764   0.984   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.491   0.852   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.007   0.581   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.530  -0.867   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.538  -2.044   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.022  -1.773   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       9.498  -0.325   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       9.029  -2.951   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.061  -3.493   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      14.046  -1.138   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      13.000   1.759   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   28                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   27                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   18   26                                             
CONECT   12   11   13   16   25                                             
CONECT   13   12   14                                                       
CONECT   14   13    7   15                                                  
CONECT   15   14                                                            
CONECT   16   12   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17   11                                                       
CONECT   19   16   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   19                                                       
CONECT   25   12                                                            
CONECT   26   11                                                            
CONECT   27    5                                                            
CONECT   28    2   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31   38                                                  
CONECT   31   30   32   37                                                  
CONECT   32   31   33   36                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   29                                                       
CONECT   35   33                                                            
CONECT   36   32                                                            
CONECT   37   31                                                            
CONECT   38   30                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₄O₉

Average Mass

536.6620 Da

Monoisotopic Mass

536.29853 Da

IUPAC Name

4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-2,5-dihydrofuran-2-one

Traditional Name

4-[(1S,2S,5S,7R,10R,11S,14R,15R,17R)-11,17-dihydroxy-2,15-dimethyl-5-{[(2S,3R,4S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]-5H-furan-2-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C29H44O9/c1-14-23(32)24(33)25(34)26(37-14)38-17-6-8-27(2)16(11-17)4-5-19-22(27)20(30)12-28(3)18(7-9-29(19,28)35)15-10-21(31)36-13-15/h10,14,16-20,22-26,30,32-35H,4-9,11-13H2,1-3H3/t14-,16+,17-,18+,19+,20+,22+,23-,24-,25+,26+,27-,28+,29-/m0/s1

InChI Key

HFMLTKBZNAPPNY-GITSYYNXSA-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
Convallaria keiskei	LOTUS Database	35616633
Dipcadi glaucum	LOTUS Database	35616633
Ornithogalum arcuatum	LOTUS Database	35616633
Rohdea japonica	Plant	KNApSAcK
Speirantha convallarioides	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
11-hydroxysteroid
11-alpha-hydroxysteroid
Hydroxysteroid
14-hydroxysteroid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Monosaccharide
2-furanone
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Dihydrofuran
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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
logP	0.62	ALOGPS
logP	1.03	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	7.18	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	145.91 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	136.1 m³·mol⁻¹	ChemAxon
Polarizability	57.3 Å³	ChemAxon
Number of Rings	6	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

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

162949413

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Rhodexin A (NP0052154)

MOL for NP0052154 (Rhodexin A)

3D MOL for NP0052154 (Rhodexin A)

3D SDF for NP0052154 (Rhodexin A)

3D-SDF for NP0052154 (Rhodexin A)

PDB for NP0052154 (Rhodexin A)

3D PDB for NP0052154 (Rhodexin A)

SMILES for NP0052154 (Rhodexin A)

INCHI for NP0052154 (Rhodexin A)

Structure for NP0052154 (Rhodexin A)

3D Structure for NP0052154 (Rhodexin A)