NP-MRD: Showing NP-Card for daphmacromine D (NP0036745)

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Record Information

Version

2.0

Created at

2021-06-20 19:50:19 UTC

Updated at

2021-06-30 00:08:33 UTC

NP-MRD ID

NP0036745

Secondary Accession Numbers

None

Natural Product Identification

Common Name

daphmacromine D

Provided By

JEOL Database JEOL Logo

Description

daphmacromine D is found in Daphniphyllum macropodum. daphmacromine D was first documented in 2012 (Cao, M., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202121503D          

 68 72  0  0  0  0            999 V2000
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M  END

     RDKit          3D

 68 72  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306202121503D          

 68 72  0  0  0  0            999 V2000
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    0.0735   -0.4338   -1.0719 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1057   -2.7001   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6808   -4.9769    0.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0036745

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C([H])([H])OC(=O)[C@]1([H])C([H])([H])[C@]23C4=C(C(=O)C([H])([H])[C@@]14[H])C([H])([H])C([H])([H])[C@]([H])(C([H])([H])N(C([H])([H])[H])C2([H])[H])[C@]31C([H])([H])O[C@@](OC([H])([H])C([H])([H])[H])(C([H])([H])C([H])([H])[H])C([H])([H])C1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H37NO5/c1-5-25(30-6-2)10-9-23(15-31-25)16-7-8-17-20(27)11-18-19(22(28)29-4)12-24(23,21(17)18)14-26(3)13-16/h16,18-19H,5-15H2,1-4H3/t16-,18+,19-,23+,24-,25+/m1/s1

> <INCHI_KEY>
ZFSSBWPJSMFMQB-RAXKZAMCSA-N

> <FORMULA>
C25H37NO5

> <MOLECULAR_WEIGHT>
431.573

> <EXACT_MASS>
431.267173295

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
48.23281763350154

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1'R,3S,5'S,6S,11'S,12'R)-6-ethoxy-6-ethyl-3'-methyl-9'-oxo-3'-azaspiro[oxane-3,15'-tetracyclo[6.5.1.1^{1,5}.0^{11,14}]pentadecan]-8'(14')-ene-12'-carboxylate

> <ALOGPS_LOGP>
2.74

> <JCHEM_LOGP>
2.4165878276666657

> <ALOGPS_LOGS>
-3.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.75606541909007

> <JCHEM_PKA_STRONGEST_BASIC>
9.265105017972592

> <JCHEM_POLAR_SURFACE_AREA>
65.07

> <JCHEM_REFRACTIVITY>
118.34889999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.73e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1'R,3S,5'S,6S,11'S,12'R)-6-ethoxy-6-ethyl-3'-methyl-9'-oxo-3'-azaspiro[oxane-3,15'-tetracyclo[6.5.1.1^{1,5}.0^{11,14}]pentadecan]-8'(14')-ene-12'-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 72  0  0  0  0  0  0  0  0999 V2000
   -3.3867    3.3859   -0.3401 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1 33  1  0
  1 34  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      -3.387   3.386  -0.340  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.751   2.642   0.931  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.569   2.507   1.714  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.643   1.562   2.795  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.790   1.932   3.765  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.911   1.047   5.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.280   1.625   3.510  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.156   1.077   2.626  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.471  -0.354   2.092  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.868  -0.237   1.415  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.873   0.232   2.317  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.540  -1.411   3.275  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.658  -1.421   4.272  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.036  -1.930   3.811  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.596  -1.220   2.642  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.992  -0.707   1.571  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.873   0.100   0.675  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.255  -0.440   0.982  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.035  -0.987   2.378  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.924  -1.268   3.168  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.211  -0.118  -0.672  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.617   0.946  -1.666  0.00  0.00           C+0
HETATM   23  O   UNK     0       3.633   1.621  -1.579  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.728   1.000  -2.695  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.056   1.965  -3.697  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.713  -0.037  -0.275  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.586  -0.855   1.050  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.294  -2.343   0.640  0.00  0.00           C+0
HETATM   29  N   UNK     0       0.174  -3.272   1.767  0.00  0.00           N+0
HETATM   30  C   UNK     0      -0.107  -4.630   1.305  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.821  -2.836   2.745  0.00  0.00           C+0
HETATM   32  H   UNK     0      -2.962   4.367  -0.105  0.00  0.00           H+0
HETATM   33  H   UNK     0      -4.265   3.524  -0.977  0.00  0.00           H+0
HETATM   34  H   UNK     0      -2.625   2.836  -0.903  0.00  0.00           H+0
HETATM   35  H   UNK     0      -4.167   1.662   0.674  0.00  0.00           H+0
HETATM   36  H   UNK     0      -4.497   3.221   1.483  0.00  0.00           H+0
HETATM   37  H   UNK     0      -4.748   1.851   3.236  0.00  0.00           H+0
HETATM   38  H   UNK     0      -3.696   2.982   4.071  0.00  0.00           H+0
HETATM   39  H   UNK     0      -3.951  -0.013   4.733  0.00  0.00           H+0
HETATM   40  H   UNK     0      -3.078   1.203   5.692  0.00  0.00           H+0
HETATM   41  H   UNK     0      -4.830   1.291   5.543  0.00  0.00           H+0
HETATM   42  H   UNK     0      -1.290   1.044   4.437  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.043   2.661   3.780  0.00  0.00           H+0
HETATM   44  H   UNK     0      -0.019   1.772   1.790  0.00  0.00           H+0
HETATM   45  H   UNK     0       0.784   1.113   3.186  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.223  -1.198   1.036  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.834   0.425   0.543  0.00  0.00           H+0
HETATM   48  H   UNK     0      -1.411  -1.156   3.893  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.779  -0.420   4.704  0.00  0.00           H+0
HETATM   50  H   UNK     0       0.363  -2.049   5.125  0.00  0.00           H+0
HETATM   51  H   UNK     0       2.010  -3.007   3.620  0.00  0.00           H+0
HETATM   52  H   UNK     0       2.720  -1.803   4.660  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.811   1.158   0.971  0.00  0.00           H+0
HETATM   54  H   UNK     0       5.005   0.355   0.990  0.00  0.00           H+0
HETATM   55  H   UNK     0       4.559  -1.249   0.312  0.00  0.00           H+0
HETATM   56  H   UNK     0       2.459  -1.098  -1.097  0.00  0.00           H+0
HETATM   57  H   UNK     0       1.275   1.938  -4.462  0.00  0.00           H+0
HETATM   58  H   UNK     0       2.084   2.971  -3.266  0.00  0.00           H+0
HETATM   59  H   UNK     0       3.012   1.717  -4.168  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.424   1.012  -0.143  0.00  0.00           H+0
HETATM   61  H   UNK     0       0.074  -0.434  -1.072  0.00  0.00           H+0
HETATM   62  H   UNK     0      -0.617  -2.381   0.029  0.00  0.00           H+0
HETATM   63  H   UNK     0       1.106  -2.700  -0.008  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.681  -4.977   0.627  0.00  0.00           H+0
HETATM   65  H   UNK     0      -0.123  -5.329   2.148  0.00  0.00           H+0
HETATM   66  H   UNK     0      -1.067  -4.697   0.782  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.831  -2.887   2.320  0.00  0.00           H+0
HETATM   68  H   UNK     0      -0.821  -3.528   3.598  0.00  0.00           H+0
CONECT    1    2   32   33   34                                             
CONECT    2    3    1   35   36                                             
CONECT    3    4    2                                                       
CONECT    4    7   11    3    5                                             
CONECT    5    4    6   37   38                                             
CONECT    6    5   39   40   41                                             
CONECT    7    8    4   42   43                                             
CONECT    8    7    9   44   45                                             
CONECT    9   12   10    8   27                                             
CONECT   10   11    9   46   47                                             
CONECT   11    4   10                                                       
CONECT   12    9   31   48   13                                             
CONECT   13   12   14   49   50                                             
CONECT   14   15   13   51   52                                             
CONECT   15   16   19   14                                                  
CONECT   16   15   17   27                                                  
CONECT   17   18   16   53   21                                             
CONECT   18   19   17   54   55                                             
CONECT   19   15   18   20                                                  
CONECT   20   19                                                            
CONECT   21   26   22   17   56                                             
CONECT   22   21   24   23                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   57   58   59                                             
CONECT   26   21   27   60   61                                             
CONECT   27   26   28   16    9                                             
CONECT   28   29   27   62   63                                             
CONECT   29   31   28   30                                                  
CONECT   30   29   64   65   66                                             
CONECT   31   12   29   67   68                                             
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    2                                                            
CONECT   36    2                                                            
CONECT   37    5                                                            
CONECT   38    5                                                            
CONECT   39    6                                                            
CONECT   40    6                                                            
CONECT   41    6                                                            
CONECT   42    7                                                            
CONECT   43    7                                                            
CONECT   44    8                                                            
CONECT   45    8                                                            
CONECT   46   10                                                            
CONECT   47   10                                                            
CONECT   48   12                                                            
CONECT   49   13                                                            
CONECT   50   13                                                            
CONECT   51   14                                                            
CONECT   52   14                                                            
CONECT   53   17                                                            
CONECT   54   18                                                            
CONECT   55   18                                                            
CONECT   56   21                                                            
CONECT   57   25                                                            
CONECT   58   25                                                            
CONECT   59   25                                                            
CONECT   60   26                                                            
CONECT   61   26                                                            
CONECT   62   28                                                            
CONECT   63   28                                                            
CONECT   64   30                                                            
CONECT   65   30                                                            
CONECT   66   30                                                            
CONECT   67   31                                                            
CONECT   68   31                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  144    0
END

RDKit          3D

68 72  0  0  0  0  0  0  0  0999 V2000
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  1 33  1  0
  1 34  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₇NO₅

Average Mass

431.5730 Da

Monoisotopic Mass

431.26717 Da

IUPAC Name

methyl (1'R,3S,5'S,6S,11'S,12'R)-6-ethoxy-6-ethyl-3'-methyl-9'-oxo-3'-azaspiro[oxane-3,15'-tetracyclo[6.5.1.1^{1,5}.0^{11,14}]pentadecan]-8'(14')-ene-12'-carboxylate

Traditional Name

methyl (1'R,3S,5'S,6S,11'S,12'R)-6-ethoxy-6-ethyl-3'-methyl-9'-oxo-3'-azaspiro[oxane-3,15'-tetracyclo[6.5.1.1^{1,5}.0^{11,14}]pentadecan]-8'(14')-ene-12'-carboxylate

CAS Registry Number

Not Available

SMILES

[H]C([H])([H])OC(=O)[C@]1([H])C([H])([H])[C@]23C4=C(C(=O)C([H])([H])[C@@]14[H])C([H])([H])C([H])([H])[C@]([H])(C([H])([H])N(C([H])([H])[H])C2([H])[H])[C@]31C([H])([H])O[C@@](OC([H])([H])C([H])([H])[H])(C([H])([H])C([H])([H])[H])C([H])([H])C1([H])[H]

InChI Identifier

InChI=1S/C25H37NO5/c1-5-25(30-6-2)10-9-23(15-31-25)16-7-8-17-20(27)11-18-19(22(28)29-4)12-24(23,21(17)18)14-26(3)13-16/h16,18-19H,5-15H2,1-4H3/t16-,18+,19-,23+,24-,25+/m1/s1

InChI Key

ZFSSBWPJSMFMQB-RAXKZAMCSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N, 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
Daphniphyllum macropodum	JEOL database	Cao, M., et al, J. Nat. Prod. 75, 1076 (2012)

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	2.74	ALOGPS
logP	2.42	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	18.76	ChemAxon
pKa (Strongest Basic)	9.27	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	65.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	118.35 m³·mol⁻¹	ChemAxon
Polarizability	48.23 Å³	ChemAxon
Number of Rings	5	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

Not Available

References

General References

Cao, M., et al. (2012). Cao, M., et al, J. Nat. Prod. 75, 1076 (2012). J. Nat. Prod..

Showing NP-Card for daphmacromine D (NP0036745)

MOL for NP0036745 (daphmacromine D)

3D MOL for NP0036745 (daphmacromine D)

3D SDF for NP0036745 (daphmacromine D)

3D-SDF for NP0036745 (daphmacromine D)

PDB for NP0036745 (daphmacromine D)

3D PDB for NP0036745 (daphmacromine D)

SMILES for NP0036745 (daphmacromine D)

INCHI for NP0036745 (daphmacromine D)

Structure for NP0036745 (daphmacromine D)

3D Structure for NP0036745 (daphmacromine D)