NP-MRD: Showing NP-Card for Cucurbitacin R (NP0081572)

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Record Information

Version

2.0

Created at

2022-04-29 02:34:27 UTC

Updated at

2022-04-29 02:34:27 UTC

NP-MRD ID

NP0081572

Secondary Accession Numbers

NP0331539

Natural Product Identification

Common Name

Cucurbitacin R

Description

23,24-Dihydrocucurbitacin D belongs to the class of organic compounds known as cucurbitacins. These are polycyclic compounds containing the tetracyclic cucurbitane nucleus skeleton, 19-(10->9b)-abeo-10alanost-5-ene (also known as 9b-methyl-19-nor lanosta-5-ene), with a variety of oxygenation functionalities at different positions. Cucurbitacin R is found in Begonia heracleifolia, Bryonia cretica, Cucumis melo , Ecballium elaterium , Neoalsomitra clavigera, Trichosanthes tricuspidata and Wilbrandia ebracteata. Cucurbitacin R was first documented in 2004 (PMID: 14752064). Based on a literature review a small amount of articles have been published on 23,24-dihydrocucurbitacin D (PMID: 34592371).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204342D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304292204342D          

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    0.9948   -0.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827   -0.2182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0976    0.5577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9098    0.7029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342    1.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1776    1.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5510    2.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3492   -0.8489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069   -0.5086    0.0000 C   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  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
  9 11  1  1  0  0  0
  8 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 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
 17 19  1  0  0  0  0
 17 20  1  0  0  0  0
 12 21  1  1  0  0  0
 12 22  1  1  0  0  0
  6 23  1  6  0  0  0
  5 24  1  1  0  0  0
  4 25  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 28 27  1  6  0  0  0
  3 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 27 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 30 36  1  6  0  0  0
  3 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081572

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O7/c1-25(2,36)12-11-21(33)30(8,37)23-19(32)14-27(5)20-10-9-16-17(13-18(31)24(35)26(16,3)4)29(20,7)22(34)15-28(23,27)6/h9,17-20,23,31-32,36-37H,10-15H2,1-8H3/t17-,18+,19-,20+,23+,27+,28-,29+,30+/m1/s1

> <INCHI_KEY>
ITMUUFDDBRYVNJ-VOKXYEOFSA-N

> <FORMULA>
C30H46O7

> <MOLECULAR_WEIGHT>
518.691

> <EXACT_MASS>
518.324353821

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
57.80545698544356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
3.15

> <JCHEM_LOGP>
2.538228639333332

> <ALOGPS_LOGS>
-4.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.48058827778939

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.799889001644043

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6327209707902703

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
140.95250000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.46e-02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.896  -2.398   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.813   1.738   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.827  -2.696   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      10.247  -4.122   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.298  -3.701   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.823  -3.490   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.349  -3.280   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.613  -1.965   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      15.034  -5.016   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.098  -0.535   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.666  -2.425   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.069  -1.700   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.505   2.629   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.332   3.252   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.028   3.743   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -0.652  -1.585   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
CONECT    1    2    3    7                                                  
CONECT    2    1                                                            
CONECT    3    1    4   28   37                                             
CONECT    4    3    5   25                                                  
CONECT    5    4    6   10   24                                             
CONECT    6    5    7    8   23                                             
CONECT    7    6    1                                                       
CONECT    8    6    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    5                                                       
CONECT   11    9                                                            
CONECT   12    8   13   21   22                                             
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
CONECT   21   12                                                            
CONECT   22   12                                                            
CONECT   23    6                                                            
CONECT   24    5                                                            
CONECT   25    4   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   33                                                  
CONECT   28   27    3   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   36                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   27   34   35                                             
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   30                                                            
CONECT   37    3                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
2beta,16alpha,20,25- Tetrahydroxy-9beta-methyl-19-nor-10alpha-lanost-5-ene-3,11,22-trione	ChEBI
2beta,16alpha,20,25-Tetrahydroxy-10alpha-cucurbit-5-ene-3,11,22-trione	ChEBI
2b,16a,20,25- Tetrahydroxy-9b-methyl-19-nor-10a-lanost-5-ene-3,11,22-trione	Generator
2Β,16α,20,25- tetrahydroxy-9β-methyl-19-nor-10α-lanost-5-ene-3,11,22-trione	Generator
2b,16a,20,25-Tetrahydroxy-10a-cucurbit-5-ene-3,11,22-trione	Generator
2Β,16α,20,25-tetrahydroxy-10α-cucurbit-5-ene-3,11,22-trione	Generator

Chemical Formula

C₃₀H₄₆O₇

Average Mass

518.6910 Da

Monoisotopic Mass

518.32435 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C30H46O7/c1-25(2,36)12-11-21(33)30(8,37)23-19(32)14-27(5)20-10-9-16-17(13-18(31)24(35)26(16,3)4)29(20,7)22(34)15-28(23,27)6/h9,17-20,23,31-32,36-37H,10-15H2,1-8H3/t17-,18+,19-,20+,23+,27+,28-,29+,30+/m1/s1

InChI Key

ITMUUFDDBRYVNJ-VOKXYEOFSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	toussaintgnaore@gmail.com	Not Available	Not Available	2023-03-17	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	toussaintgnaore@gmail.com	Not Available	Not Available	2023-03-17	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	toussaintgnaore@gmail.com	Not Available	Not Available	2023-03-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	toussaintgnaore@gmail.com	Not Available	Not Available	2023-03-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	toussaintgnaore@gmail.com	Not Available	Not Available	2023-03-17	View Spectrum

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
Begonia heracleifolia	LOTUS Database	35616633
Bryonia cretica	LOTUS Database	35616633
Cucumis melo	Plant	KNApSAcK
Ecballium elaterium	Plant	KNApSAcK
Neoalsomitra clavigera	LOTUS Database	35616633
Trichosanthes tricuspidata	LOTUS Database	35616633
Wilbrandia ebracteata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cucurbitacins. These are polycyclic compounds containing the tetracyclic cucurbitane nucleus skeleton, 19-(10->9b)-abeo-10alanost-5-ene (also known as 9b-methyl-19-nor lanosta-5-ene), with a variety of oxygenation functionalities at different positions.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cucurbitacins

Direct Parent

Cucurbitacins

Alternative Parents

Substituents

Cucurbitacin skeleton
Triterpenoid
25-hydroxysteroid
22-oxosteroid
21-oxosteroid
20-hydroxysteroid
14-alpha-methylsteroid
3-oxo-delta-5-steroid
16-hydroxysteroid
16-alpha-hydroxysteroid
3-oxosteroid
Oxosteroid
11-oxosteroid
2-hydroxysteroid
Hydroxysteroid
Delta-5-steroid
Acyloin
Alpha-hydroxy ketone
Cyclic alcohol
Tertiary alcohol
Cyclic ketone
Secondary alcohol
Ketone
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Alcohol
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

23,24-dihydrocucurbitacin (CHEBI:62218 )

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	3.15	ALOGPS
logP	2.54	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	12.8	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	132.13 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	140.95 m³·mol⁻¹	ChemAxon
Polarizability	57.81 Å³	ChemAxon
Number of Rings	4	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

Not Available

Chemspider ID

157100

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

180535

PDB ID

Not Available

ChEBI ID

62218

Good Scents ID

Not Available

References

General References

Uushona NE, Dziwornu GA, Mkwanazi N, Kaschula CH, Sunassee SN, de Villiers A: New dihydroxycucurbitacin D's from the Namib desert endemic plant Acanthosicyos horridus (!nara). Fitoterapia. 2021 Nov;155:105041. doi: 10.1016/j.fitote.2021.105041. Epub 2021 Sep 28. [PubMed:34592371 ]
Park CS, Lim H, Han KJ, Baek SH, Sohn HO, Lee DW, Kim YG, Yun HY, Baek KJ, Kwon NS: Inhibition of nitric oxide generation by 23,24-dihydrocucurbitacin D in mouse peritoneal macrophages. J Pharmacol Exp Ther. 2004 May;309(2):705-10. doi: 10.1124/jpet.103.063693. Epub 2004 Jan 29. [PubMed:14752064 ]

Showing NP-Card for Cucurbitacin R (NP0081572)

MOL for NP0081572 (Cucurbitacin R)

3D MOL for NP0081572 (Cucurbitacin R)

3D SDF for NP0081572 (Cucurbitacin R)

3D-SDF for NP0081572 (Cucurbitacin R)

PDB for NP0081572 (Cucurbitacin R)

3D PDB for NP0081572 (Cucurbitacin R)

SMILES for NP0081572 (Cucurbitacin R)

INCHI for NP0081572 (Cucurbitacin R)

Structure for NP0081572 (Cucurbitacin R)

3D Structure for NP0081572 (Cucurbitacin R)