NP-MRD: Showing NP-Card for Dendrocyin (NP0074538)

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Record Information

Version

2.0

Created at

2022-04-28 19:49:27 UTC

Updated at

2022-04-28 19:49:27 UTC

NP-MRD ID

NP0074538

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dendrocyin

Description

Dendrocyin belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton. Dendrocyin is found in Dendrosicyos socotrana. Dendrocyin was first documented in 2004 (PMID: 15451315). Based on a literature review very few articles have been published on Dendrocyin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282221492D          

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M  END

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M  END


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   -0.5535   -1.1398    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3004   -0.3546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5061   -0.1811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0764   -0.0743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5020    0.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3601   -1.3133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9136   -0.7015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7201   -0.8750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7890   -1.1784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5607    0.9312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8685    1.4085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0307   -0.9107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5466   -0.5086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5311    1.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8025    2.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2632    0.7029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10  5  1  1  0  0  0
 10 11  1  0  0  0  0
  1 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 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
 20 26  1  6  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 24 29  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 20 32  1  6  0  0  0
 18 33  1  6  0  0  0
 16 34  1  6  0  0  0
 15 35  1  1  0  0  0
  9 36  1  1  0  0  0
  4 37  1  0  0  0  0
  4 38  1  0  0  0  0
  3 39  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0074538

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCO[C@@H]1CC(=O)[C@@](C)(OC1(C)C)[C@H]1[C@H](O)C[C@@]2(C)[C@@H]3CC=C4[C@@H](CC(=O)[C@@H](O)C4(C)C)[C@]3(C)C(=O)C[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C32H48O7/c1-10-38-24-14-22(35)32(9,39-28(24,4)5)25-20(34)15-29(6)21-12-11-17-18(13-19(33)26(37)27(17,2)3)31(21,8)23(36)16-30(25,29)7/h11,18,20-21,24-26,34,37H,10,12-16H2,1-9H3/t18-,20-,21+,24-,25+,26-,29+,30-,31+,32-/m1/s1

> <INCHI_KEY>
GPFCTBZKSDGUFM-ZPJCXYQLSA-N

> <FORMULA>
C32H48O7

> <MOLECULAR_WEIGHT>
544.729

> <EXACT_MASS>
544.340003886

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
60.627560094797715

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,5S,10S,11S,13R,14R,15R)-14-[(2S,5R)-5-ethoxy-2,6,6-trimethyl-3-oxooxan-2-yl]-5,13-dihydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-ene-4,17-dione

> <ALOGPS_LOGP>
4.40

> <JCHEM_LOGP>
3.4248436189999985

> <ALOGPS_LOGS>
-5.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.506795261742635

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.908143659688545

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8838219767530164

> <JCHEM_POLAR_SURFACE_AREA>
110.13000000000001

> <JCHEM_REFRACTIVITY>
147.94390000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,10S,11S,13R,14R,15R)-14-[(2S,5R)-5-ethoxy-2,6,6-trimethyl-3-oxooxan-2-yl]-5,13-dihydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-ene-4,17-dione

> <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      11.519  -0.407   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      12.512  -1.585   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      12.042   1.041   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.049   2.218   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.533   1.947   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.541   3.125   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.025   2.854   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.502   1.405   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.494   0.228   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.010   0.499   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.003  -0.678   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.971  -1.221   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       7.964  -2.398   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.455  -1.492   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.462  -0.314   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.986   1.134   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.770   2.079   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.495   1.215   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.923  -0.264   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.978  -1.480   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.506  -2.946   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.539  -4.088   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.000  -3.270   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.033  -2.128   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.561  -0.662   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.945  -0.338   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -2.009  -0.139   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.937   0.831   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.539  -2.451   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -3.572  -1.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.078  -1.633   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.339  -2.200   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.047   1.738   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.355   2.629   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.791  -1.700   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       8.487  -0.949   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      12.191   3.252   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      10.831   3.743   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      13.558   1.312   0.000  0.00  0.00           O+0
CONECT    1    2    3   11                                                  
CONECT    2    1                                                            
CONECT    3    1    4   39                                                  
CONECT    4    3    5   37   38                                             
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10   12   36                                             
CONECT   10    9    5   11                                                  
CONECT   11   10    1                                                       
CONECT   12    9   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   19   35                                             
CONECT   16   15    8   17   34                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   33                                                  
CONECT   19   18   15   20                                                  
CONECT   20   19   21   26   32                                             
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26   27   28                                             
CONECT   26   25   20                                                       
CONECT   27   25                                                            
CONECT   28   25                                                            
CONECT   29   24   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   20                                                            
CONECT   33   18                                                            
CONECT   34   16                                                            
CONECT   35   15                                                            
CONECT   36    9                                                            
CONECT   37    4                                                            
CONECT   38    4                                                            
CONECT   39    3                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₂H₄₈O₇

Average Mass

544.7290 Da

Monoisotopic Mass

544.34000 Da

IUPAC Name

(1R,2R,5S,10S,11S,13R,14R,15R)-14-[(2S,5R)-5-ethoxy-2,6,6-trimethyl-3-oxooxan-2-yl]-5,13-dihydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-ene-4,17-dione

Traditional Name

(1R,2R,5S,10S,11S,13R,14R,15R)-14-[(2S,5R)-5-ethoxy-2,6,6-trimethyl-3-oxooxan-2-yl]-5,13-dihydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-ene-4,17-dione

CAS Registry Number

Not Available

SMILES

CCO[C@@H]1CC(=O)[C@@](C)(OC1(C)C)[C@H]1[C@H](O)C[C@@]2(C)[C@@H]3CC=C4[C@@H](CC(=O)[C@@H](O)C4(C)C)[C@]3(C)C(=O)C[C@]12C

InChI Identifier

InChI=1S/C32H48O7/c1-10-38-24-14-22(35)32(9,39-28(24,4)5)25-20(34)15-29(6)21-12-11-17-18(13-19(33)26(37)27(17,2)3)31(21,8)23(36)16-30(25,29)7/h11,18,20-21,24-26,34,37H,10,12-16H2,1-9H3/t18-,20-,21+,24-,25+,26-,29+,30-,31+,32-/m1/s1

InChI Key

GPFCTBZKSDGUFM-ZPJCXYQLSA-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
Dendrosicyos socotrana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Oxosteroids

Direct Parent

11-oxosteroids

Alternative Parents

Substituents

3-hydroxy-delta-5-steroid
3-hydroxysteroid
14-alpha-methylsteroid
Hydroxysteroid
11-oxosteroid
16-alpha-hydroxysteroid
3-alpha-hydroxysteroid
16-hydroxysteroid
Delta-5-steroid
Oxane
Cyclic alcohol
Secondary alcohol
Ketone
Cyclic ketone
Organoheterocyclic compound
Oxacycle
Ether
Dialkyl ether
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
Alcohol
Organic oxide
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	4.4	ALOGPS
logP	3.42	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	12.91	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	110.13 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	147.94 m³·mol⁻¹	ChemAxon
Polarizability	60.63 Å³	ChemAxon
Number of Rings	5	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

C00035824

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

101356882

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hussein HA, Abdel-Halim OB, Marwan el-SM, El-Gamal AA, Mosana R: Dendrocyin: an isocucurbitacin with novel cyclic side chain from Dendrosicyos socotrana. Phytochemistry. 2004 Sep;65(18):2551-6. doi: 10.1016/j.phytochem.2004.07.016. [PubMed:15451315 ]

Showing NP-Card for Dendrocyin (NP0074538)

MOL for NP0074538 (Dendrocyin)

3D MOL for NP0074538 (Dendrocyin)

3D SDF for NP0074538 (Dendrocyin)

3D-SDF for NP0074538 (Dendrocyin)

PDB for NP0074538 (Dendrocyin)

3D PDB for NP0074538 (Dendrocyin)

SMILES for NP0074538 (Dendrocyin)

INCHI for NP0074538 (Dendrocyin)

Structure for NP0074538 (Dendrocyin)

3D Structure for NP0074538 (Dendrocyin)