NP-MRD: Showing NP-Card for (1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate (NP0165308)

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Record Information

Version

2.0

Created at

2022-09-03 00:24:20 UTC

Updated at

2022-09-03 00:24:21 UTC

NP-MRD ID

NP0165308

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate

Description

Gniditrin belongs to the class of organic compounds known as rhamnofolane and daphnane diterpenoids. These are diterpenoids with a structure based on one the rhamnofolane or daphnane skeleton. The rhamnofolane and daphnane skeletons are closely related, being formally derived from casbane by two cyclizations (6,10 and 5,14) followed by cleavage of the 1,15 (daphnane) or 2,15 (rhamnofolane) cyclopropane bonds. (1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate is found in Thymelaea hirsuta. (1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate was first documented in 2007 (PMID: 17673184). Based on a literature review a small amount of articles have been published on Gniditrin (PMID: 22148316) (PMID: 35977604) (PMID: 35891417) (PMID: 23923651).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032202242D          

 47 53  0  0  1  0            999 V2000
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   -0.1048   -0.9539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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 35 76  1  1
 33 72  1  1
 34 73  1  0
 34 74  1  0
 34 75  1  0
 14 58  1  6
 15 59  1  1
 16 60  1  6
 19 61  1  0
 19 62  1  0
 20 63  1  0
 21 64  1  1
 22 65  1  0
 24 66  1  0
 30 71  1  6
 29 70  1  0
 28 67  1  0
 28 68  1  0
 28 69  1  0
  3 50  1  0
  3 51  1  0
  3 52  1  0
  1 48  1  0
  1 49  1  0
  8 53  1  0
  9 54  1  0
 10 55  1  0
 11 56  1  0
 12 57  1  0
M  END


  Mrv1652309032202242D          

 47 53  0  0  1  0            999 V2000
   -1.6487   -3.3123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4991   -2.4547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3966   -2.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5534   -2.0169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8891   -1.2388    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1048   -0.9539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5583   -0.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2741   -0.1326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7276    0.6646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3594    1.3886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4317    1.2666    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0841    0.5184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0110   -1.9829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6465   -2.0371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9411   -1.3680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4360   -0.7080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0238   -0.1290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2285    0.0905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9782    0.7220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8379    0.9781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4749    0.4261    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9491    1.3369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2574    0.0461    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0099    1.0561    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9779    0.4480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9136    1.4397    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5827   -0.1131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4938    0.0759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360   -0.8617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4169   -0.7633    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1165   -1.3927    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5097   -0.5897    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3012   -2.5364    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9280   -3.1518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4614   -2.7524    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9544   -3.5315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6645   -4.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1946   -4.9595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1480   -4.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4304   -5.2455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2429   -5.3885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5253   -6.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3378   -6.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -7.0818    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4327   -7.2248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7152   -8.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5277   -8.1430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  4  2  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  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
 11 12  2  0  0  0  0
  7 12  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 30 29  1  6  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 15 31  1  0  0  0  0
 31 32  1  1  0  0  0
  6 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
  4 35  1  0  0  0  0
 35 36  1  1  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 39 40  2  0  0  0  0
 40 41  1  0  0  0  0
 41 42  2  0  0  0  0
 42 43  1  0  0  0  0
 43 44  2  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0165308

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC\C=C\C=C\C=C\C(=O)O[C@@H]1[C@@H](C)[C@@]23OC4(OC(C2C2O[C@]2(CO)[C@@H](O)[C@@]2(O)[C@H]3C=C(C)C2=O)[C@]1(O4)C(C)=C)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C37H42O10/c1-6-7-8-9-10-11-15-18-26(39)43-29-23(5)36-25-19-22(4)28(40)34(25,42)32(41)33(20-38)30(44-33)27(36)31-35(29,21(2)3)46-37(45-31,47-36)24-16-13-12-14-17-24/h8-19,23,25,27,29-32,38,41-42H,2,6-7,20H2,1,3-5H3/b9-8+,11-10+,18-15+/t23-,25-,27?,29-,30?,31?,32-,33+,34-,35+,36+,37?/m1/s1

> <INCHI_KEY>
NEIGQRKMHFDLTK-SGAAPIRTSA-N

> <FORMULA>
C37H42O10

> <MOLECULAR_WEIGHT>
646.733

> <EXACT_MASS>
646.277797552

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
89

> <JCHEM_AVERAGE_POLARIZABILITY>
67.93142950703914

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,6S,7S,8R,16S,17R,18R)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0^{1,11}.0^{2,6}.0^{8,10}.0^{12,16}]nonadec-3-en-17-yl (2E,4E,6E)-deca-2,4,6-trienoate

> <ALOGPS_LOGP>
4.00

> <JCHEM_LOGP>
5.063019778333334

> <ALOGPS_LOGS>
-4.78

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.327888189956163

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.64635001670891

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1497130859472193

> <JCHEM_POLAR_SURFACE_AREA>
144.28

> <JCHEM_REFRACTIVITY>
173.13250000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.07e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,6S,7S,8R,16S,17R,18R)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0^{1,11}.0^{2,6}.0^{8,10}.0^{12,16}]nonadec-3-en-17-yl (2E,4E,6E)-deca-2,4,6-trienoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.077  -6.183   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.798  -4.582   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.474  -4.655   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.033  -3.765   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.660  -2.312   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.196  -1.781   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.042  -0.293   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.378  -0.247   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.225   1.241   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.538   2.592   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.806   2.364   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.157   0.968   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.021  -3.701   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.207  -3.803   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.757  -2.554   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.681  -1.322   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.778  -0.241   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.293   0.169   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.693   1.348   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.297   1.826   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.886   0.795   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.772   2.496   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.480   0.086   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.018   1.971   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -1.825   0.836   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.705   2.687   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -2.954  -0.211   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.655   0.142   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.307  -1.609   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.778  -1.425   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.217  -2.600   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.951  -1.101   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.562  -4.735   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.732  -5.883   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.861  -5.138   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.782  -6.592   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -1.240  -8.078   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -2.230  -9.258   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       0.276  -8.345   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       0.803  -9.792   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       2.320 -10.059   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       2.847 -11.505   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       4.364 -11.772   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       4.891 -13.219   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.408 -13.486   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       6.935 -14.933   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       8.452 -15.200   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   14   35                                             
CONECT    5    4    6                                                       
CONECT    6    5    7   13   32                                             
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7                                                       
CONECT   13    6   14                                                       
CONECT   14   13    4   15                                                  
CONECT   15   14   16   31                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   18                                                       
CONECT   18   17   16   19   21                                             
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25   30                                             
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   23   31                                                  
CONECT   31   30   15   32   33                                             
CONECT   32   31    6                                                       
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    4   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46                                                            
MASTER        0    0    0    0    0    0    0    0   47    0  106    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₇H₄₂O₁₀

Average Mass

646.7330 Da

Monoisotopic Mass

646.27780 Da

IUPAC Name

(1R,2R,6S,7S,8R,16S,17R,18R)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0^{1,11}.0^{2,6}.0^{8,10}.0^{12,16}]nonadec-3-en-17-yl (2E,4E,6E)-deca-2,4,6-trienoate

Traditional Name

CAS Registry Number

Not Available

SMILES

CCC\C=C\C=C\C=C\C(=O)O[C@@H]1[C@@H](C)[C@@]23OC4(OC(C2C2O[C@]2(CO)[C@@H](O)[C@@]2(O)[C@H]3C=C(C)C2=O)[C@]1(O4)C(C)=C)C1=CC=CC=C1

InChI Identifier

InChI=1S/C37H42O10/c1-6-7-8-9-10-11-15-18-26(39)43-29-23(5)36-25-19-22(4)28(40)34(25,42)32(41)33(20-38)30(44-33)27(36)31-35(29,21(2)3)46-37(45-31,47-36)24-16-13-12-14-17-24/h8-19,23,25,27,29-32,38,41-42H,2,6-7,20H2,1,3-5H3/b9-8+,11-10+,18-15+/t23-,25-,27?,29-,30?,31?,32-,33+,34-,35+,36+,37?/m1/s1

InChI Key

NEIGQRKMHFDLTK-SGAAPIRTSA-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
Thymelaea hirsuta	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as rhamnofolane and daphnane diterpenoids. These are diterpenoids with a structure based on one the rhamnofolane or daphnane skeleton. The rhamnofolane and daphnane skeletons are closely related, being formally derived from casbane by two cyclizations (6,10 and 5,14) followed by cleavage of the 1,15 (daphnane) or 2,15 (rhamnofolane) cyclopropane bonds.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Rhamnofolane and daphnane diterpenoids

Alternative Parents

Substituents

Daphnane diterpenoid
Ortho ester
Fatty acid ester
Dioxepane
Carboxylic acid orthoester
1,3-dioxepane
Fatty acyl
Benzenoid
Monocyclic benzene moiety
Meta-dioxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Cyclic alcohol
Meta-dioxolane
Secondary alcohol
Orthocarboxylic acid derivative
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
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	4	ALOGPS
logP	5.06	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	11.65	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	144.28 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	173.13 m³·mol⁻¹	ChemAxon
Polarizability	67.93 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00003433

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

118701514

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Vidal V, Potterat O, Louvel S, Hamy F, Mojarrab M, Sanglier JJ, Klimkait T, Hamburger M: Library-based discovery and characterization of daphnane diterpenes as potent and selective HIV inhibitors in Daphne gnidium. J Nat Prod. 2012 Mar 23;75(3):414-9. doi: 10.1021/np200855d. Epub 2011 Dec 8. [PubMed:22148316 ]
Zhang Y, Zhang H, Hua S, Ma L, Chen C, Liu X, Jiang L, Yang H, Zhang P, Yu D, Guo Y, Tan X, Liu J: Identification of two herbal compounds with potential cholesterol-lowering activity. Biochem Pharmacol. 2007 Sep 15;74(6):940-7. doi: 10.1016/j.bcp.2007.06.020. Epub 2007 Jun 20. [PubMed:17673184 ]
Guo R, Li Q, Mi SH, Jia SH, Yao GD, Lin B, Huang XX, Liu YY, Song SJ: Target isolation of cytotoxic diterpenoid esters and orthoesters from Daphne tangutica maxim based on molecular networking. Phytochemistry. 2022 Nov;203:113358. doi: 10.1016/j.phytochem.2022.113358. Epub 2022 Aug 14. [PubMed:35977604 ]
Tembeni B, Sciorillo A, Invernizzi L, Klimkait T, Urda L, Moyo P, Naidoo-Maharaj D, Levitties N, Gyampoh K, Zu G, Yuan Z, Mounzer K, Nkabinde S, Nkabinde M, Gqaleni N, Tietjen I, Montaner LJ, Maharaj V: HPLC-Based Purification and Isolation of Potent Anti-HIV and Latency Reversing Daphnane Diterpenes from the Medicinal Plant Gnidia sericocephala (Thymelaeaceae). Viruses. 2022 Jun 30;14(7):1437. doi: 10.3390/v14071437. [PubMed:35891417 ]
Gorick C, Melzig MF: Gniditrin is the main diterpenoid constituent in the bark of Daphne mezereum L. Pharmazie. 2013 Jul;68(7):640-2. [PubMed:23923651 ]
LOTUS database [Link]

Showing NP-Card for (1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate (NP0165308)

MOL for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

3D MOL for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

3D SDF for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

3D-SDF for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

PDB for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

3D PDB for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

SMILES for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

INCHI for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

Structure for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)

3D Structure for NP0165308 ((1r,2r,6s,7s,8r,16s,17r,18r)-6,7-dihydroxy-8-(hydroxymethyl)-4,18-dimethyl-5-oxo-14-phenyl-16-(prop-1-en-2-yl)-9,13,15,19-tetraoxahexacyclo[12.4.1.0¹,¹¹.0²,⁶.0⁸,¹⁰.0¹²,¹⁶]nonadec-3-en-17-yl (2e,4e,6e)-deca-2,4,6-trienoate)