NP-MRD: Showing NP-Card for Cucurbitacin P (NP0052180)

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Record Information

Version

2.0

Created at

2022-04-27 23:19:54 UTC

Updated at

2022-04-27 23:19:54 UTC

NP-MRD ID

NP0052180

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cucurbitacin P

Description

Cucurbitacin p 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. Thus, cucurbitacin p is considered to be a sterol. Cucurbitacin P is found in Brandegea bigelovii and Wilbrandia ebracteata. Cucurbitacin P was first documented in 2022 (PMID: 35227014). Based on a literature review very few articles have been published on Cucurbitacin p (PMID: 35211103).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304282201192D          

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M  END

     RDKit          3D

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M  END

  Mrv1652304282201192D          

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   -1.4747   -1.0526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7109   -1.2992    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4083   -0.2865    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
    6.7026   -0.8489    0.0000 O   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  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  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
  1 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 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
 14 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 27  1  0  0  0  0
 19 28  1  6  0  0  0
 19 29  1  6  0  0  0
 17 30  1  6  0  0  0
 15 31  1  6  0  0  0
 14 32  1  1  0  0  0
  8 33  1  1  0  0  0
  3 34  1  0  0  0  0
  3 35  1  0  0  0  0
  2 36  1  6  0  0  0
  1 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0052180

> <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@@H](O)C4(C)C)[C@]3(C)C(=O)C[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O7/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/h9,17-20,23-24,31-32,35-37H,10-15H2,1-8H3/t17-,18-,19-,20+,23+,24-,27+,28-,29+,30+/m1/s1

> <INCHI_KEY>
VVBWBGOEAVGFTN-SYJGCRHZSA-N

> <FORMULA>
C30H48O7

> <MOLECULAR_WEIGHT>
520.707

> <EXACT_MASS>
520.340003886

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
85

> <JCHEM_AVERAGE_POLARIZABILITY>
58.27087908070682

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.79

> <JCHEM_LOGP>
1.7708632473333321

> <ALOGPS_LOGS>
-3.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.635068398031116

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.850000119929042

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6327209707902703

> <JCHEM_POLAR_SURFACE_AREA>
135.29000000000002

> <JCHEM_REFRACTIVITY>
141.64410000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.61e-02 g/l

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

> <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  C   UNK     0      12.042   1.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.049   2.218   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.533   1.947   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.541   3.125   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.025   2.854   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.502   1.405   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.494   0.228   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.010   0.499   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.003  -0.678   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.971  -1.221   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       7.964  -2.398   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.455  -1.492   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.462  -0.314   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.986   1.134   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.770   2.079   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.495   1.215   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.923  -0.264   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.978  -1.480   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.033  -2.696   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.613  -4.122   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.493  -2.485   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.438  -3.701   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.963  -3.490   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -4.489  -3.280   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.174  -5.016   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.753  -1.965   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.194  -2.425   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.762  -0.535   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.047   1.738   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.355   2.629   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.791  -1.700   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.487  -0.949   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.191   3.252   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.831   3.743   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      13.558   1.312   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      12.512  -1.585   0.000  0.00  0.00           O+0
CONECT    1    2   10   37                                                  
CONECT    2    1    3   36                                                  
CONECT    3    2    4   34   35                                             
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   11   33                                             
CONECT    9    8    4   10                                                  
CONECT   10    9    1                                                       
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   18   32                                             
CONECT   15   14    7   16   31                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   14   19                                                  
CONECT   19   18   20   28   29                                             
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24                                                            
CONECT   28   19                                                            
CONECT   29   19                                                            
CONECT   30   17                                                            
CONECT   31   15                                                            
CONECT   32   14                                                            
CONECT   33    8                                                            
CONECT   34    3                                                            
CONECT   35    3                                                            
CONECT   36    2                                                            
CONECT   37    1                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₈O₇

Average Mass

520.7070 Da

Monoisotopic Mass

520.34000 Da

IUPAC Name

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

Traditional Name

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

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@@H](O)C4(C)C)[C@]3(C)C(=O)C[C@]12C

InChI Identifier

InChI=1S/C30H48O7/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/h9,17-20,23-24,31-32,35-37H,10-15H2,1-8H3/t17-,18-,19-,20+,23+,24-,27+,28-,29+,30+/m1/s1

InChI Key

VVBWBGOEAVGFTN-SYJGCRHZSA-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
Brandegea bigelovii	Plant	KNApSAcK
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
3-alpha-hydroxysteroid
16-hydroxysteroid
16-alpha-hydroxysteroid
14-alpha-methylsteroid
3-hydroxysteroid
Oxosteroid
Hydroxysteroid
11-oxosteroid
2-hydroxysteroid
3-hydroxy-delta-5-steroid
Delta-5-steroid
Acyloin
Alpha-hydroxy ketone
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Ketone
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Alcohol
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

cucurbitacin (CHEBI:3951 )
Cholesterol and derivatives (C08804 )
Cycloartane (C08804 )
Cholesterol and derivatives (LMST01010114 )

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	2.79	ALOGPS
logP	1.77	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	12.85	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	141.64 m³·mol⁻¹	ChemAxon
Polarizability	58.27 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

C00003692

Chemspider ID

390404

KEGG Compound ID

C08804

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441822

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liu Z, Kumar M, Kabra A: Cucurbitacin B exerts neuroprotection in a murine Alzheimer's disease model by modulating oxidative stress, inflammation, and neurotransmitter levels. Front Biosci (Landmark Ed). 2022 Feb 17;27(2):71. doi: 10.31083/j.fbl2702071. [PubMed:35227014 ]
Pofu KM, Mashela PW: Interactive Effects of Filamentous Fungi and Cucurbitacin Phytonematicide on Growth of Cowpea and Suppression of Meloidogyne enterolobii. Front Microbiol. 2022 Feb 8;13:765051. doi: 10.3389/fmicb.2022.765051. eCollection 2022. [PubMed:35211103 ]

Showing NP-Card for Cucurbitacin P (NP0052180)

MOL for NP0052180 (Cucurbitacin P)

3D MOL for NP0052180 (Cucurbitacin P)

3D SDF for NP0052180 (Cucurbitacin P)

3D-SDF for NP0052180 (Cucurbitacin P)

PDB for NP0052180 (Cucurbitacin P)

3D PDB for NP0052180 (Cucurbitacin P)

SMILES for NP0052180 (Cucurbitacin P)

INCHI for NP0052180 (Cucurbitacin P)

Structure for NP0052180 (Cucurbitacin P)

3D Structure for NP0052180 (Cucurbitacin P)