NP-MRD: Showing NP-Card for Vernomigeodiin D (NP0351083)

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Record Information

Version

2.0

Created at

2025-05-28 15:00:58 UTC

Updated at

2025-12-23 08:35:08 UTC

NP-MRD ID

NP0351083

Natural Product DOI

https://doi.org/10.57994/4072

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Vernomigeodiin D

Description

Based on a literature review very few articles have been published on Vernomigeodiin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03102317252D          

 34 37  0  0  1  0            999 V2000
    7.2632    0.7029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4511    0.5577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1708   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3587   -0.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8269    0.2673    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5466   -0.5086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1072    1.0432    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5754    1.6739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7633    1.5287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4830    0.7528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0148    0.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7345   -0.6539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9224   -0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3905   -0.1684    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0307   -0.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6708    0.6076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2027   -0.0231    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0195    1.1139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3367    0.6509    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5607    0.9312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5660   -0.1416    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0596   -0.7929    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3705   -1.5571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2424   -0.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2640   -1.3314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0469   -2.0955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0812   -1.2185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3921   -0.4543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5876   -1.8698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0939   -2.5212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2389   -1.3635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9363   -2.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3875    1.8191    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9193    1.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  5 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 10  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 19 18  1  0  0  0  0
 19 20  1  6  0  0  0
 21 19  1  0  0  0  0
 21 14  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 25  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
  7 33  1  6  0  0  0
  7 34  1  0  0  0  0
  2 34  1  0  0  0  0
M  END


  Mrv2104 03102317252D          

 34 37  0  0  1  0            999 V2000
    7.2632    0.7029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4511    0.5577    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1708   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3587   -0.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8269    0.2673    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5466   -0.5086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1072    1.0432    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5754    1.6739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7633    1.5287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4830    0.7528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0148    0.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7345   -0.6539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9224   -0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3905   -0.1684    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0307   -0.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6708    0.6076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2027   -0.0231    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0195    1.1139    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3367    0.6509    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5607    0.9312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5660   -0.1416    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0596   -0.7929    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3705   -1.5571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2424   -0.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2640   -1.3314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0469   -2.0955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0812   -1.2185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3921   -0.4543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5876   -1.8698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0939   -2.5212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2389   -1.3635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9363   -2.3762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3875    1.8191    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9193    1.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  5 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 10  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 19 18  1  0  0  0  0
 19 20  1  6  0  0  0
 21 19  1  0  0  0  0
 21 14  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 25  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
  7 33  1  6  0  0  0
  7 34  1  0  0  0  0
  2 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0351083

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12C[C@@H](O)[C@H]([C@H](C)CC(O)[C@@H](C)C(C)(C)O)[C@@]1(C)CC=C1C2=CC[C@@]2([H])C[C@@H](O)CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H46O4/c1-16(13-23(30)17(2)26(3,4)32)25-24(31)15-22-20-8-7-18-14-19(29)9-11-27(18,5)21(20)10-12-28(22,25)6/h8,10,16-19,22-25,29-32H,7,9,11-15H2,1-6H3/t16-,17-,18+,19+,22+,23?,24-,25+,27+,28+/m1/s1

> <INCHI_KEY>
XDAIGYXIXFOPGC-BHVHHDIGSA-N

> <FORMULA>
C28H46O4

> <MOLECULAR_WEIGHT>
446.672

> <EXACT_MASS>
446.339609961

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
54.5100726225612

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R)-6-[(1R,2R,3aR,5aS,7S,9aS,11aS)-2,7-dihydroxy-9a,11a-dimethyl-1H,2H,3H,3aH,5H,5aH,6H,7H,8H,9H,9aH,11H,11aH-cyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptane-2,4-diol

> <JCHEM_LOGP>
2.9472410936666655

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.332409786983527

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.622753505956878

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5072759518184909

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
130.93739999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R)-6-[(1R,2R,3aR,5aS,7S,9aS,11aS)-2,7-dihydroxy-9a,11a-dimethyl-1H,2H,3H,3aH,5H,5aH,6H,7H,8H,9H,11H-cyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptane-2,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-23         0                                  
HETATM    1  O   UNK     0      13.558   1.312   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      12.042   1.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.519  -0.407   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.003  -0.678   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.010   0.499   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.487  -0.949   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.533   1.947   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.541   3.125   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.025   2.854   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.502   1.405   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.494   0.228   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.971  -1.221   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.455  -1.492   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.462  -0.314   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.791  -1.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.986   1.134   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0       5.978  -0.043   0.000  0.00  0.00           H+0
HETATM   18  C   UNK     0       3.770   2.079   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.495   1.215   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.047   1.738   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.923  -0.264   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.978  -1.480   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.558  -2.907   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.452  -1.269   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.493  -2.485   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.088  -3.912   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -2.018  -2.275   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.599  -0.848   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.963  -3.490   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.909  -4.706   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.179  -2.545   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.748  -4.436   0.000  0.00  0.00           C+0
HETATM   33  H   UNK     0      10.057   3.396   0.000  0.00  0.00           H+0
HETATM   34  C   UNK     0      11.049   2.218   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7   11                                             
CONECT    6    5                                                            
CONECT    7    5    8   33   34                                             
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10    5   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   21                                             
CONECT   15   14                                                            
CONECT   16   14   10   17   18                                             
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   14   22                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31   32                                             
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   29                                                            
CONECT   33    7                                                            
CONECT   34    7    2                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₆O₄

Average Mass

446.6720 Da

Monoisotopic Mass

446.33961 Da

IUPAC Name

(3R,6R)-6-[(1R,2R,3aR,5aS,7S,9aS,11aS)-2,7-dihydroxy-9a,11a-dimethyl-1H,2H,3H,3aH,5H,5aH,6H,7H,8H,9H,9aH,11H,11aH-cyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptane-2,4-diol

Traditional Name

(3R,6R)-6-[(1R,2R,3aR,5aS,7S,9aS,11aS)-2,7-dihydroxy-9a,11a-dimethyl-1H,2H,3H,3aH,5H,5aH,6H,7H,8H,9H,11H-cyclopenta[a]phenanthren-1-yl]-2,3-dimethylheptane-2,4-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]12C[C@@H](O)[C@H]([C@H](C)CC(O)[C@@H](C)C(C)(C)O)[C@@]1(C)CC=C1C2=CC[C@@]2([H])C[C@@H](O)CC[C@]12C

InChI Identifier

InChI=1S/C28H46O4/c1-16(13-23(30)17(2)26(3,4)32)25-24(31)15-22-20-8-7-18-14-19(29)9-11-27(18,5)21(20)10-12-28(22,25)6/h8,10,16-19,22-25,29-32H,7,9,11-15H2,1-6H3/t16-,17-,18+,19+,22+,23?,24-,25+,27+,28+/m1/s1

InChI Key

XDAIGYXIXFOPGC-BHVHHDIGSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	[email protected]	University of Szeged	Judit Hohmann	2025-05-28	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Vernoniastrum migeodii		Not Available

Chemical Taxonomy

Classification

Not classified

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	2.95	ChemAxon
pKa (Strongest Acidic)	14.62	ChemAxon
pKa (Strongest Basic)	-0.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	130.94 m³·mol⁻¹	ChemAxon
Polarizability	54.51 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Vernomigeodiin D (NP0351083)

MOL for NP0351083 (Vernomigeodiin D)

3D MOL for NP0351083 (Vernomigeodiin D)

3D SDF for NP0351083 (Vernomigeodiin D)

3D-SDF for NP0351083 (Vernomigeodiin D)

PDB for NP0351083 (Vernomigeodiin D)

3D PDB for NP0351083 (Vernomigeodiin D)

SMILES for NP0351083 (Vernomigeodiin D)

INCHI for NP0351083 (Vernomigeodiin D)

Structure for NP0351083 (Vernomigeodiin D)

3D Structure for NP0351083 (Vernomigeodiin D)