NP-MRD: Showing NP-Card for Tabernaesine D (NP0353005)

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Record Information

Version

2.0

Created at

2026-02-16 21:00:25 UTC

Updated at

2026-02-17 00:02:09 UTC

NP-MRD ID

NP0353005

Natural Product DOI

https://doi.org/10.57994/7327

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tabernaesine D

Description

Tabernaesine D was first documented in 2020 (PMID: 33112136).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03172318132D          

 60 72  0  0  1  0            999 V2000
    1.5902    2.8867    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8874    2.4547    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1845    2.0227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5183    1.5907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410    2.4154    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1387    1.8467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9613    1.9103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4276    1.2298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0715    0.4857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5379   -0.1949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3604   -0.1312    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8268   -0.8117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6494   -0.7481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7166    0.6129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5391    0.6766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2489    0.4220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928   -0.3222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826    1.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2072    1.1980    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    5.6552    1.9743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
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  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
  6 18  1  0  0  0  0
 18 19  1  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  2  0  0  0  0
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 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 26 32  1  0  0  0  0
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 33 34  1  0  0  0  0
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 56 60  1  0  0  0  0
  2 60  1  0  0  0  0
M  END


  Mrv2104 03172318132D          

 60 72  0  0  1  0            999 V2000
    1.5902    2.8867    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8874    2.4547    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1845    2.0227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5183    1.5907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5410    2.4154    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -2.4276    1.2298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5379   -0.1949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.8268   -0.8117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0353005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@]34CC(=O)O[C@H]3CCN3CC[C@]5([C@H]43)C3=CC=C(CN(CC)CC)C(O)=C3N(C[C@@]3(CN4CC[C@@]67[C@@H]4[C@]4(CCO[C@@H]34)CC(C(=O)OC)=C6NC3=C7C=CC=C3)C1)[C@@]25O

> <INCHI_IDENTIFIER>
InChI=1S/C47H57N5O7/c1-4-49(5-2)24-27-10-11-31-35(36(27)54)52-26-42(20-28-21-44-23-34(53)59-33(44)12-16-50-18-14-46(31,40(44)50)47(28,52)56)25-51-17-13-45-30-8-6-7-9-32(30)48-37(45)29(38(55)57-3)22-43(39(45)51)15-19-58-41(42)43/h6-11,28,33,39-41,48,54,56H,4-5,12-26H2,1-3H3/t28-,33+,39+,40+,41+,42+,43+,44+,45+,46-,47-/m1/s1

> <INCHI_KEY>
KCWRHWBPKUJETJ-ZAWUBLFESA-N

> <FORMULA>
C47H57N5O7

> <MOLECULAR_WEIGHT>
804.001

> <EXACT_MASS>
803.425799195

$$$$

HEADER    PROTEIN                                 17-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAR-23         0                                  
HETATM    1  H   UNK     0       2.968   5.388   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       1.656   4.582   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.344   3.776   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.968   2.969   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.010   4.509   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.126   3.447   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.661   3.566   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.532   2.296   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.867   0.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.737  -0.364   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -6.273  -0.245   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -7.143  -1.515   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.679  -1.396   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.938   1.144   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.473   1.263   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.331   0.788   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.667  -0.601   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.461   2.058   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.387   2.236   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       1.741   1.503   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.053   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.191   3.348   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       5.658   2.882   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       5.989   1.378   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.457   0.912   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.785   1.691   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.936   0.668   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       9.320  -0.743   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      11.398   1.154   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.708   2.663   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.556   3.685   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.095   3.199   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.353   2.164   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.440   3.404   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.787  -0.592   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.650  -1.630   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.980  -3.135   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       8.448  -3.600   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       8.778  -5.105   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       5.843  -4.173   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       5.391  -1.102   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.851   0.340   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       3.384   0.805   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       2.487  -0.447   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       3.401  -1.686   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.862  -1.200   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       3.011   3.849   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -2.461   3.993   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -3.400   5.213   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -1.052   6.048   0.000  0.00  0.00           C+0
HETATM   51  N   UNK     0      -2.407   6.781   0.000  0.00  0.00           N+0
HETATM   52  C   UNK     0      -2.449   8.321   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -1.137   9.127   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       0.217   8.394   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       1.668   8.910   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       0.260   6.854   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       1.613   6.837   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       2.607   7.689   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       4.147   7.732   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       1.614   6.121   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   47   60                                             
CONECT    3    2    4    5   19                                             
CONECT    4    3                                                            
CONECT    5    3    6   48   50                                             
CONECT    6    5    7   18                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15                                                       
CONECT   15   14                                                            
CONECT   16    9   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    6   19                                                  
CONECT   19   18    3   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   43   47                                             
CONECT   22   21   23                                                       
CONECT   23   22   24   34                                                  
CONECT   24   23   25   42                                                  
CONECT   25   24   26   33   35                                             
CONECT   26   25   27   32                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   35                                                       
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   26                                                       
CONECT   33   25   34                                                       
CONECT   34   33   23                                                       
CONECT   35   25   28   36                                                  
CONECT   36   35   37   41                                                  
CONECT   37   36   38   40                                                  
CONECT   38   37   39                                                       
CONECT   39   38                                                            
CONECT   40   37                                                            
CONECT   41   36   42                                                       
CONECT   42   24   41   43   46                                             
CONECT   43   42   21   44                                                  
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   42                                                       
CONECT   47   21    2                                                       
CONECT   48    5   49                                                       
CONECT   49   48   51                                                       
CONECT   50    5   51   56                                                  
CONECT   51   50   49   52                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54   58                                                       
CONECT   56   54   50   57   60                                             
CONECT   57   56   58                                                       
CONECT   58   57   55   59                                                  
CONECT   59   58                                                            
CONECT   60   56    2                                                       
MASTER        0    0    0    0    0    0    0    0   60    0  144    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₇H₅₇N₅O₇

Average Mass

804.0010 Da

Monoisotopic Mass

803.42580 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@]34CC(=O)O[C@H]3CCN3CC[C@]5([C@H]43)C3=CC=C(CN(CC)CC)C(O)=C3N(C[C@@]3(CN4CC[C@@]67[C@@H]4[C@]4(CCO[C@@H]34)CC(C(=O)OC)=C6NC3=C7C=CC=C3)C1)[C@@]25O

InChI Identifier

InChI=1S/C47H57N5O7/c1-4-49(5-2)24-27-10-11-31-35(36(27)54)52-26-42(20-28-21-44-23-34(53)59-33(44)12-16-50-18-14-46(31,40(44)50)47(28,52)56)25-51-17-13-45-30-8-6-7-9-32(30)48-37(45)29(38(55)57-3)22-43(39(45)51)15-19-58-41(42)43/h6-11,28,33,39-41,48,54,56H,4-5,12-26H2,1-3H3/t28-,33+,39+,40+,41+,42+,43+,44+,45+,46-,47-/m1/s1

InChI Key

KCWRHWBPKUJETJ-ZAWUBLFESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.0, Acetone-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150.0, Acetone-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-16	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Tabernaemontana pachysiphon		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

External Links

Not Available

References

General References

Showing NP-Card for Tabernaesine D (NP0353005)

MOL for NP0353005 (Tabernaesine D)

3D MOL for NP0353005 (Tabernaesine D)

3D SDF for NP0353005 (Tabernaesine D)

3D-SDF for NP0353005 (Tabernaesine D)

PDB for NP0353005 (Tabernaesine D)

3D PDB for NP0353005 (Tabernaesine D)

SMILES for NP0353005 (Tabernaesine D)

INCHI for NP0353005 (Tabernaesine D)

Structure for NP0353005 (Tabernaesine D)

3D Structure for NP0353005 (Tabernaesine D)