NP-MRD: Showing NP-Card for Daphmacrine (NP0076395)

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Record Information

Version

2.0

Created at

2022-04-28 21:32:27 UTC

Updated at

2022-04-28 21:32:27 UTC

NP-MRD ID

NP0076395

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daphmacrine

Description

(1R,2S,5R,8R)-1,5-dimethyl-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-1-methyl-14-(propan-2-yl)-12-azapentacyclo[8.6.0.0²,¹³.0³,⁷.0⁷,¹²]Hexadecan-2-yl]ethyl}-7-oxo-6-oxabicyclo[3.2.1]Octan-2-yl acetate belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Daphmacrine is found in Daphniphyllum oldhami. Based on a literature review very few articles have been published on (1R,2S,5R,8R)-1,5-dimethyl-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-1-methyl-14-(propan-2-yl)-12-azapentacyclo[8.6.0.0²,¹³.0³,⁷.0⁷,¹²]Hexadecan-2-yl]ethyl}-7-oxo-6-oxabicyclo[3.2.1]Octan-2-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223322D          

 37 43  0  0  1  0            999 V2000
    3.3085    1.6660    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    2.9317   -0.0261    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 33 35  1  0  0  0  0
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  1 37  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282223322D          

 37 43  0  0  1  0            999 V2000
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    0.9286    0.2202    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1785    0.8121    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3457    0.1751    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1746   -0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5631   -1.0014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3119   -0.6549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5078    0.1465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0034    0.7993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    1.8524    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5723   -1.5266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2346    0.2870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9542   -0.1514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9348   -0.9762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6782    0.2442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5504    1.3900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2777    2.5787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  6  5  1  6  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9  4  1  1  0  0  0
  9 10  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  1 16  1  0  0  0  0
 14 17  1  6  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
  2 20  1  1  0  0  0
 20 21  1  0  0  0  0
 22 21  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 23 29  1  0  0  0  0
 29 30  2  0  0  0  0
 27 31  1  1  0  0  0
 24 32  1  6  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 23 36  1  1  0  0  0
  1 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0076395

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@]45CCC[C@H]4[C@@]2(CC[C@H]2[C@@]4(C)CC[C@H](OC(C)=O)[C@]2(C)C(=O)O4)[C@H]1N5C3

> <INCHI_IDENTIFIER>
InChI=1S/C32H49NO4/c1-19(2)22-10-14-28(4)21-9-16-31-13-7-8-24(31)32(28,26(22)33(31)18-21)17-11-23-29(5)15-12-25(36-20(3)34)30(23,6)27(35)37-29/h19,21-26H,7-18H2,1-6H3/t21-,22-,23+,24-,25+,26+,28+,29-,30-,31-,32+/m1/s1

> <INCHI_KEY>
HHUKBFWZEBQMEU-JNZYVOHRSA-N

> <FORMULA>
C32H49NO4

> <MOLECULAR_WEIGHT>
511.747

> <EXACT_MASS>
511.366159062

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
86

> <JCHEM_AVERAGE_POLARIZABILITY>
58.68550388510673

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,5R,8R)-1,5-dimethyl-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-1-methyl-14-(propan-2-yl)-12-azapentacyclo[8.6.0.0^{2,13}.0^{3,7}.0^{7,12}]hexadecan-2-yl]ethyl}-7-oxo-6-oxabicyclo[3.2.1]octan-2-yl acetate

> <ALOGPS_LOGP>
5.98

> <JCHEM_LOGP>
5.6851577153333315

> <ALOGPS_LOGS>
-6.43

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
12.775140150622766

> <JCHEM_POLAR_SURFACE_AREA>
55.839999999999996

> <JCHEM_REFRACTIVITY>
142.3953

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.89e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,5R,8R)-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-14-isopropyl-1-methyl-12-azapentacyclo[8.6.0.0^{2,13}.0^{3,7}.0^{7,12}]hexadecan-2-yl]ethyl}-1,5-dimethyl-7-oxo-6-oxabicyclo[3.2.1]octan-2-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.996   3.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.326   2.378   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.300   0.549   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.188   0.041   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       6.329   1.323   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.637   1.634   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.240  -0.482   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.858  -0.291   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.615   1.051   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.814   2.574   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.585   3.579   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.306   2.710   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.025   0.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.856   0.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.484   2.112   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.597   3.419   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.898  -0.601   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.481  -0.713   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.719  -2.191   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.182   0.975   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.146   1.830   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.466   0.625   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.104   1.775   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.914   0.619   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.644  -0.897   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.709  -1.632   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.127  -1.032   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.543   0.451   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.642   1.701   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.608   3.642   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.738  -2.578   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.523   0.946   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -3.826   0.076   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -3.725  -1.461   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -5.207   0.757   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.120   2.993   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.931   4.882   0.000  0.00  0.00           C+0
CONECT    1    2    6   16   37                                             
CONECT    2    1    3   10   20                                             
CONECT    3    2    4   14                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10   13                                             
CONECT   10    9    2   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9                                                       
CONECT   14    3   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15    1                                                       
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24   29   36                                             
CONECT   24   23   25   32                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22   28   31                                             
CONECT   28   27   29                                                       
CONECT   29   28   23   30                                                  
CONECT   30   29                                                            
CONECT   31   27                                                            
CONECT   32   24   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   23                                                            
CONECT   37    1                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   86    0
END

View in JSmol

Synonyms

Value	Source
(1R,2S,5R,8R)-1,5-Dimethyl-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-1-methyl-14-(propan-2-yl)-12-azapentacyclo[8.6.0.0,.0,.0,]hexadecan-2-yl]ethyl}-7-oxo-6-oxabicyclo[3.2.1]octan-2-yl acetic acid	Generator

Chemical Formula

C₃₂H₄₉NO₄

Average Mass

511.7470 Da

Monoisotopic Mass

511.36616 Da

IUPAC Name

(1R,2S,5R,8R)-1,5-dimethyl-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-1-methyl-14-(propan-2-yl)-12-azapentacyclo[8.6.0.0^{2,13}.0^{3,7}.0^{7,12}]hexadecan-2-yl]ethyl}-7-oxo-6-oxabicyclo[3.2.1]octan-2-yl acetate

Traditional Name

(1R,2S,5R,8R)-8-{2-[(1S,2R,3S,7R,10S,13S,14R)-14-isopropyl-1-methyl-12-azapentacyclo[8.6.0.0^{2,13}.0^{3,7}.0^{7,12}]hexadecan-2-yl]ethyl}-1,5-dimethyl-7-oxo-6-oxabicyclo[3.2.1]octan-2-yl acetate

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@]45CCC[C@H]4[C@@]2(CC[C@H]2[C@@]4(C)CC[C@H](OC(C)=O)[C@]2(C)C(=O)O4)[C@H]1N5C3

InChI Identifier

InChI=1S/C32H49NO4/c1-19(2)22-10-14-28(4)21-9-16-31-13-7-8-24(31)32(28,26(22)33(31)18-21)17-11-23-29(5)15-12-25(36-20(3)34)30(23,6)27(35)37-29/h19,21-26H,7-18H2,1-6H3/t21-,22-,23+,24-,25+,26+,28+,29-,30-,31-,32+/m1/s1

InChI Key

HHUKBFWZEBQMEU-JNZYVOHRSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Daphniphyllum oldhamii	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Sesquiterpenoid
Azaspirodecane
Indolizidine
Indole or derivatives
Caprolactone
Oxepane
Azepane
N-alkylpyrrolidine
Piperidine
Gamma butyrolactone
Dicarboxylic acid or derivatives
Tetrahydrofuran
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Lactone
Carboxylic acid ester
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	5.98	ALOGPS
logP	5.69	ChemAxon
logS	-6.4	ALOGPS
pKa (Strongest Basic)	12.78	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	55.84 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	142.4 m³·mol⁻¹	ChemAxon
Polarizability	58.69 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

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

162852161

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Daphmacrine (NP0076395)

MOL for NP0076395 (Daphmacrine)

3D MOL for NP0076395 (Daphmacrine)

3D SDF for NP0076395 (Daphmacrine)

3D-SDF for NP0076395 (Daphmacrine)

PDB for NP0076395 (Daphmacrine)

3D PDB for NP0076395 (Daphmacrine)

SMILES for NP0076395 (Daphmacrine)

INCHI for NP0076395 (Daphmacrine)

Structure for NP0076395 (Daphmacrine)

3D Structure for NP0076395 (Daphmacrine)