NP-MRD: Showing NP-Card for 5,12beta-dihydroxycinobufagin (NP0033967)

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Record Information

Version

2.0

Created at

2021-06-20 17:50:06 UTC

Updated at

2021-06-30 00:04:03 UTC

NP-MRD ID

NP0033967

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,12beta-dihydroxycinobufagin

Provided By

JEOL Database JEOL Logo

Description

5,12Beta-Dihydroxycinobufagin belongs to the class of organic compounds known as bufanolides and derivatives. These are steroid lactones containing a pyran-2-one moiety linked to the C17 atom of a cyclopenta[a]phenanthrene derivative. 5,12beta-dihydroxycinobufagin is found in Syncephalastrum racemosum. 5,12beta-dihydroxycinobufagin was first documented in 2008 (PMID: 18558746). Based on a literature review very few articles have been published on 5,12beta-Dihydroxycinobufagin.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202119503D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306202119503D          

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  2  3  2  0  0  0  0
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 17 47  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0033967

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])C([H])([H])C([H])([H])[C@]2(C([H])([H])[H])[C@@]3([H])C([H])([H])[C@@]([H])(O[H])[C@]4(C([H])([H])[H])[C@@]([H])(C5=C([H])OC(=O)C([H])=C5[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]5([H])O[C@@]45[C@]3([H])C([H])([H])C([H])([H])[C@]2(O[H])C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C26H34O8/c1-13(27)33-21-20(14-4-5-19(30)32-12-14)24(3)18(29)10-17-16(26(24)22(21)34-26)7-9-25(31)11-15(28)6-8-23(17,25)2/h4-5,12,15-18,20-22,28-29,31H,6-11H2,1-3H3/t15-,16+,17-,18+,20-,21+,22+,23+,24+,25-,26+/m0/s1

> <INCHI_KEY>
MJGBQRFJIZZZFQ-CIXQQPKYSA-N

> <FORMULA>
C26H34O8

> <MOLECULAR_WEIGHT>
474.55

> <EXACT_MASS>
474.225368055

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.27327343650025

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,4R,5R,6S,7S,8R,10S,11R,14S,16S)-8,14,16-trihydroxy-7,11-dimethyl-6-(2-oxo-2H-pyran-5-yl)-3-oxapentacyclo[8.8.0.0^{2,4}.0^{2,7}.0^{11,16}]octadecan-5-yl acetate

> <ALOGPS_LOGP>
1.35

> <JCHEM_LOGP>
0.3448321643333324

> <ALOGPS_LOGS>
-3.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.668209139516371

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.066428027951314

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7258844383092162

> <JCHEM_POLAR_SURFACE_AREA>
125.82000000000002

> <JCHEM_REFRACTIVITY>
119.77609999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,4R,5R,6S,7S,8R,10S,11R,14S,16S)-8,14,16-trihydroxy-7,11-dimethyl-6-(6-oxopyran-3-yl)-3-oxapentacyclo[8.8.0.0^{2,4}.0^{2,7}.0^{11,16}]octadecan-5-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 73  0  0  0  0  0  0  0  0999 V2000
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 14  6  1  0
 34  5  1  0
  5  6  1  0
 22 21  1  0
 26 27  1  0
 20 21  1  0
 30 31  1  1
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 17 47  1  0
M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0      -0.363   6.420   1.438  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.023   5.096   1.205  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.220   4.884   1.333  0.00  0.00           O+0
HETATM    4  O   UNK     0      -0.097   4.172   0.831  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.615   2.854   0.647  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.951   2.070   1.964  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.233   2.517   3.240  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.990   2.449   4.474  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.455   2.843   5.634  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.921   3.365   5.697  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.399   3.727   6.767  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.616   3.425   4.521  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.014   3.000   3.325  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.748   0.547   1.542  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.255  -0.349   2.694  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.075   0.008   0.934  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.033  -0.198   1.969  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.885  -1.298   0.148  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.846  -1.153  -0.992  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.509  -0.642  -0.418  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.562  -0.449  -1.521  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.729  -1.687  -2.393  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.403  -2.191  -2.989  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.675  -3.413  -3.700  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.112  -1.196  -4.063  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.440  -1.631  -4.686  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.260  -2.798  -5.486  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.500  -1.902  -3.623  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.007  -2.882  -2.560  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.673  -2.456  -1.872  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.258  -3.662  -0.983  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.278   0.598   0.417  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.436   1.404   0.671  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.379   2.003  -0.089  0.00  0.00           C+0
HETATM   35  H   UNK     0       0.372   6.331   2.242  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.113   6.765   0.517  0.00  0.00           H+0
HETATM   37  H   UNK     0      -1.118   7.154   1.736  0.00  0.00           H+0
HETATM   38  H   UNK     0      -1.509   2.905   0.010  0.00  0.00           H+0
HETATM   39  H   UNK     0      -2.020   2.251   2.148  0.00  0.00           H+0
HETATM   40  H   UNK     0      -2.006   2.063   4.448  0.00  0.00           H+0
HETATM   41  H   UNK     0      -0.998   2.799   6.569  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.712   3.126   2.509  0.00  0.00           H+0
HETATM   43  H   UNK     0      -0.950  -0.340   3.540  0.00  0.00           H+0
HETATM   44  H   UNK     0      -0.142  -1.391   2.380  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.731  -0.037   3.054  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.502   0.751   0.248  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.854  -0.527   1.561  0.00  0.00           H+0
HETATM   48  H   UNK     0      -1.611  -2.101   0.839  0.00  0.00           H+0
HETATM   49  H   UNK     0      -2.861  -1.585  -0.259  0.00  0.00           H+0
HETATM   50  H   UNK     0      -1.229  -0.355  -1.640  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.905  -1.402   0.266  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.304   0.405  -2.156  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.531  -0.205  -1.070  0.00  0.00           H+0
HETATM   54  H   UNK     0       2.442  -1.473  -3.200  0.00  0.00           H+0
HETATM   55  H   UNK     0       2.207  -2.481  -1.806  0.00  0.00           H+0
HETATM   56  H   UNK     0       1.289  -3.951  -3.168  0.00  0.00           H+0
HETATM   57  H   UNK     0      -0.235  -0.191  -3.648  0.00  0.00           H+0
HETATM   58  H   UNK     0       0.634  -1.129  -4.866  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.800  -0.845  -5.360  0.00  0.00           H+0
HETATM   60  H   UNK     0      -0.575  -3.343  -5.041  0.00  0.00           H+0
HETATM   61  H   UNK     0      -2.804  -0.961  -3.152  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.394  -2.327  -4.096  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.873  -3.863  -3.037  0.00  0.00           H+0
HETATM   64  H   UNK     0      -2.800  -3.036  -1.820  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.670  -3.482  -0.435  0.00  0.00           H+0
HETATM   66  H   UNK     0      -1.033  -3.906  -0.250  0.00  0.00           H+0
HETATM   67  H   UNK     0      -0.111  -4.570  -1.579  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.533   2.247  -1.126  0.00  0.00           H+0
CONECT    1    2   35   36   37                                             
CONECT    2    4    1    3                                                  
CONECT    3    2                                                            
CONECT    4    5    2                                                       
CONECT    5   34    6    4   38                                             
CONECT    6   14    5    7   39                                             
CONECT    7    6    8   13                                                  
CONECT    8    7    9   40                                                  
CONECT    9    8   10   41                                                  
CONECT   10    9   12   11                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13    7   12   42                                                  
CONECT   14    6   15   16   32                                             
CONECT   15   14   43   44   45                                             
CONECT   16   14   18   17   46                                             
CONECT   17   16   47                                                       
CONECT   18   19   16   48   49                                             
CONECT   19   20   18   30   50                                             
CONECT   20   21   19   32   51                                             
CONECT   21   22   20   52   53                                             
CONECT   22   21   23   54   55                                             
CONECT   23   24   25   30   22                                             
CONECT   24   23   56                                                       
CONECT   25   23   26   57   58                                             
CONECT   26   27   28   25   59                                             
CONECT   27   26   60                                                       
CONECT   28   26   29   61   62                                             
CONECT   29   30   28   63   64                                             
CONECT   30   31   29   23   19                                             
CONECT   31   30   65   66   67                                             
CONECT   32   34   33   20   14                                             
CONECT   33   32   34                                                       
CONECT   34    5   32   33   68                                             
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    5                                                            
CONECT   39    6                                                            
CONECT   40    8                                                            
CONECT   41    9                                                            
CONECT   42   13                                                            
CONECT   43   15                                                            
CONECT   44   15                                                            
CONECT   45   15                                                            
CONECT   46   16                                                            
CONECT   47   17                                                            
CONECT   48   18                                                            
CONECT   49   18                                                            
CONECT   50   19                                                            
CONECT   51   20                                                            
CONECT   52   21                                                            
CONECT   53   21                                                            
CONECT   54   22                                                            
CONECT   55   22                                                            
CONECT   56   24                                                            
CONECT   57   25                                                            
CONECT   58   25                                                            
CONECT   59   26                                                            
CONECT   60   27                                                            
CONECT   61   28                                                            
CONECT   62   28                                                            
CONECT   63   29                                                            
CONECT   64   29                                                            
CONECT   65   31                                                            
CONECT   66   31                                                            
CONECT   67   31                                                            
CONECT   68   34                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  146    0
END

RDKit          3D

68 73  0  0  0  0  0  0  0  0999 V2000
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 17 47  1  0
M  END

View in JSmol

Synonyms

Value	Source
5,12b-Dihydroxycinobufagin	Generator
5,12Β-dihydroxycinobufagin	Generator

Chemical Formula

C₂₆H₃₄O₈

Average Mass

474.5500 Da

Monoisotopic Mass

474.22537 Da

IUPAC Name

(1R,2S,4R,5R,6S,7S,8R,10S,11R,14S,16S)-8,14,16-trihydroxy-7,11-dimethyl-6-(2-oxo-2H-pyran-5-yl)-3-oxapentacyclo[8.8.0.0^{2,4}.0^{2,7}.0^{11,16}]octadecan-5-yl acetate

Traditional Name

(1R,2S,4R,5R,6S,7S,8R,10S,11R,14S,16S)-8,14,16-trihydroxy-7,11-dimethyl-6-(6-oxopyran-3-yl)-3-oxapentacyclo[8.8.0.0^{2,4}.0^{2,7}.0^{11,16}]octadecan-5-yl acetate

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])C([H])([H])C([H])([H])[C@]2(C([H])([H])[H])[C@@]3([H])C([H])([H])[C@@]([H])(O[H])[C@]4(C([H])([H])[H])[C@@]([H])(C5=C([H])OC(=O)C([H])=C5[H])[C@@]([H])(OC(=O)C([H])([H])[H])[C@@]5([H])O[C@@]45[C@]3([H])C([H])([H])C([H])([H])[C@]2(O[H])C1([H])[H]

InChI Identifier

InChI=1S/C26H34O8/c1-13(27)33-21-20(14-4-5-19(30)32-12-14)24(3)18(29)10-17-16(26(24)22(21)34-26)7-9-25(31)11-15(28)6-8-23(17,25)2/h4-5,12,15-18,20-22,28-29,31H,6-11H2,1-3H3/t15-,16+,17-,18+,20-,21+,22+,23+,24+,25-,26+/m0/s1

InChI Key

MJGBQRFJIZZZFQ-CIXQQPKYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Syncephalastrum racemosum	JEOL database	Ma, X. -C., et al, J. Nat. Prod. 71, 1268 (2008)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bufanolides and derivatives. These are steroid lactones containing a pyran-2-one moiety linked to the C17 atom of a cyclopenta[a]phenanthrene derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Bufanolides and derivatives

Alternative Parents

Substituents

Bufanolide-skeleton
Steroid ester
Naphthopyran
Naphthalene
Pyranone
Pyran
Oxane
Cyclic alcohol
Heteroaromatic compound
Tertiary alcohol
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Polyol
Organic oxygen compound
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Organooxygen 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	1.35	ALOGPS
logP	0.34	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	14.07	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	125.82 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	119.78 m³·mol⁻¹	ChemAxon
Polarizability	49.27 Å³	ChemAxon
Number of Rings	6	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

23342442

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24970584

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ma XC, Xin XL, Liu KX, Han J, Guo DA: Microbial transformation of cinobufagin by Syncephalastrum racemosum. J Nat Prod. 2008 Jul;71(7):1268-70. doi: 10.1021/np800210a. Epub 2008 Jun 18. [PubMed:18558746 ]
Ma, X. -C., et al. (2008). Ma, X. -C., et al, J. Nat. Prod. 71, 1268 (2008). J. Nat. Prod..

Showing NP-Card for 5,12beta-dihydroxycinobufagin (NP0033967)

MOL for NP0033967 (5,12beta-dihydroxycinobufagin)

3D MOL for NP0033967 (5,12beta-dihydroxycinobufagin)

3D SDF for NP0033967 (5,12beta-dihydroxycinobufagin)

3D-SDF for NP0033967 (5,12beta-dihydroxycinobufagin)

PDB for NP0033967 (5,12beta-dihydroxycinobufagin)

3D PDB for NP0033967 (5,12beta-dihydroxycinobufagin)

SMILES for NP0033967 (5,12beta-dihydroxycinobufagin)

INCHI for NP0033967 (5,12beta-dihydroxycinobufagin)

Structure for NP0033967 (5,12beta-dihydroxycinobufagin)

3D Structure for NP0033967 (5,12beta-dihydroxycinobufagin)