NP-MRD: Showing NP-Card for Desmondiin D (NP0333439)

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Record Information

Version

2.0

Created at

2024-06-20 17:06:45 UTC

Updated at

2024-11-01 00:17:24 UTC

NP-MRD ID

NP0333439

Natural Product DOI

https://doi.org/10.57994/2881

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Desmondiin D

Description

Desmondiin D belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. Based on a literature review very few articles have been published on Desmondiin D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03042319412D          

 33 36  0  0  1  0            999 V2000
    1.0950   -3.4826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0950   -4.3076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8094   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2384   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9529   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6673   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9529   -3.4826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3805   -4.7201    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2943   -5.5405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5127   -5.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9252   -4.9976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3732   -4.3845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2399   -3.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281   -3.5999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4351   -3.4284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4101   -5.6650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7322   -4.8261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9871   -4.0415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7941   -3.8699    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2421   -3.2568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3461   -4.4830    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0912   -5.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2842   -5.4392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0293   -6.2238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982   -5.0961    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1531   -4.3115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1819   -5.1360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9701   -4.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4080   -3.5269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2150   -3.3553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8560   -2.9138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0490   -3.0853    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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  9  2  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 17  1  1  0  0  0
 12 18  1  0  0  0  0
 18 19  2  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 18 24  1  0  0  0  0
 24 25  2  0  0  0  0
 22 26  1  6  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 30 27  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 20 33  1  0  0  0  0
M  END


  Mrv2104 03042319412D          

 33 36  0  0  1  0            999 V2000
    1.0950   -3.4826    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0950   -4.3076    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8094   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2384   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9529   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6673   -4.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9529   -3.4826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3805   -4.7201    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2943   -5.5405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5127   -5.7121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9252   -4.9976    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3732   -4.3845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2399   -3.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6281   -3.5999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4351   -3.4284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4101   -5.6650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7322   -4.8261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9871   -4.0415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7941   -3.8699    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2421   -3.2568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3461   -4.4830    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0912   -5.2676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2842   -5.4392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0293   -6.2238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982   -5.0961    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1531   -4.3115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1819   -5.1360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9701   -4.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4080   -3.5269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2150   -3.3553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8560   -2.9138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0490   -3.0853    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
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  9  2  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 17  1  1  0  0  0
 12 18  1  0  0  0  0
 18 19  2  0  0  0  0
 16 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 18 24  1  0  0  0  0
 24 25  2  0  0  0  0
 22 26  1  6  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 30 27  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 20 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333439

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC(=O)C3=C(CC[C@@]4(C)[C@@H](CC[C@]34C)[C@@H](C)CCCC(C)=O)[C@@]1(C)CC[C@H](O)C2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C29H46O3/c1-18(9-8-10-19(2)30)20-11-16-29(7)25-21(12-15-28(20,29)6)27(5)14-13-24(32)26(3,4)23(27)17-22(25)31/h18,20,23-24,32H,8-17H2,1-7H3/t18-,20-,23-,24-,27+,28-,29+/m0/s1

> <INCHI_KEY>
HICJXVPLWGTUSB-LOEQCYBFSA-N

> <FORMULA>
C29H46O3

> <MOLECULAR_WEIGHT>
442.684

> <EXACT_MASS>
442.344695341

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
53.28576299635487

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3aS,5aR,7S,9aS,11aS)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-1-[(2S)-6-oxoheptan-2-yl]-1H,2H,3H,3aH,4H,5H,5aH,6H,7H,8H,9H,9aH,10H,11H,11aH-cyclopenta[a]phenanthren-4-one

> <JCHEM_LOGP>
5.7227646373333325

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.643324485500845

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.618725644141033

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7785518089707554

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
130.45479999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3aS,5aR,7S,9aS,11aS)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-1-[(2S)-6-oxoheptan-2-yl]-1H,2H,3H,5H,5aH,7H,8H,9H,10H,11H-cyclopenta[a]phenanthren-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAR-23         0                                  
HETATM    1  C   UNK     0       2.044  -6.501   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.044  -8.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.378  -8.811   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.711  -8.041   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.045  -8.811   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.379  -8.041   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.712  -8.811   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.379  -6.501   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.710  -8.811   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.549 -10.342   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.957 -10.663   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.727  -9.329   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.697  -8.184   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.448  -7.154   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.172  -6.720   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.679  -6.400   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.632 -10.575   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.233  -9.009   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.709  -7.544   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.216  -7.224   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.185  -6.079   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.246  -8.368   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.770  -9.833   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.264 -10.153   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -3.788 -11.618   0.000  0.00  0.00           O+0
HETATM   26  H   UNK     0      -7.277  -9.513   0.000  0.00  0.00           H+0
HETATM   27  C   UNK     0      -7.752  -8.048   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -7.806  -9.587   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.277  -8.262   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.228  -6.583   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -9.735  -6.263   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -7.198  -5.439   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.692  -5.759   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    2   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17   18                                             
CONECT   13   12    9   14   15                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   19                                                       
CONECT   17   12                                                            
CONECT   18   12   19   24                                                  
CONECT   19   18   16   20                                                  
CONECT   20   19   21   22   33                                             
CONECT   21   20                                                            
CONECT   22   20   23   26   27                                             
CONECT   23   22   24                                                       
CONECT   24   23   18   25                                                  
CONECT   25   24                                                            
CONECT   26   22                                                            
CONECT   27   22   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   20                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₆O₃

Average Mass

442.6840 Da

Monoisotopic Mass

442.34470 Da

IUPAC Name

(1S,3aS,5aR,7S,9aS,11aS)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-1-[(2S)-6-oxoheptan-2-yl]-1H,2H,3H,3aH,4H,5H,5aH,6H,7H,8H,9H,9aH,10H,11H,11aH-cyclopenta[a]phenanthren-4-one

Traditional Name

(1S,3aS,5aR,7S,9aS,11aS)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-1-[(2S)-6-oxoheptan-2-yl]-1H,2H,3H,5H,5aH,7H,8H,9H,10H,11H-cyclopenta[a]phenanthren-4-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC(=O)C3=C(CC[C@@]4(C)[C@@H](CC[C@]34C)[C@@H](C)CCCC(C)=O)[C@@]1(C)CC[C@H](O)C2(C)C

InChI Identifier

InChI=1S/C29H46O3/c1-18(9-8-10-19(2)30)20-11-16-29(7)25-21(12-15-28(20,29)6)27(5)14-13-24(32)26(3,4)23(27)17-22(25)31/h18,20,23-24,32H,8-17H2,1-7H3/t18-,20-,23-,24-,27+,28-,29+/m0/s1

InChI Key

HICJXVPLWGTUSB-LOEQCYBFSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	hohmann.judit@szte.hu	University of Szeged	Judit Hohmann	2024-06-20	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
Euphorbia desmondii		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as vitamin d and derivatives. These are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin D and derivatives

Alternative Parents

Substituents

Triterpenoid
25-oxosteroid
7-oxosteroid
3-beta-hydroxysteroid
Oxosteroid
Hydroxysteroid
3-hydroxysteroid
Cyclohexenone
Alpha-branched alpha,beta-unsaturated-ketone
Alpha,beta-unsaturated ketone
Enone
Cyclic alcohol
Acryloyl-group
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	5.72	ChemAxon
pKa (Strongest Acidic)	19.62	ChemAxon
pKa (Strongest Basic)	-0.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	130.45 m³·mol⁻¹	ChemAxon
Polarizability	53.29 Å³	ChemAxon
Number of Rings	4	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Desmondiin D (NP0333439)

MOL for NP0333439 (Desmondiin D)

3D MOL for NP0333439 (Desmondiin D)

3D SDF for NP0333439 (Desmondiin D)

3D-SDF for NP0333439 (Desmondiin D)

PDB for NP0333439 (Desmondiin D)

3D PDB for NP0333439 (Desmondiin D)

SMILES for NP0333439 (Desmondiin D)

INCHI for NP0333439 (Desmondiin D)

Structure for NP0333439 (Desmondiin D)

3D Structure for NP0333439 (Desmondiin D)