NP-MRD: Showing NP-Card for Bryodulcosigenin (NP0052173)

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Record Information

Version

2.0

Created at

2022-04-27 23:19:35 UTC

Updated at

2022-04-27 23:19:35 UTC

NP-MRD ID

NP0052173

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bryodulcosigenin

Description

Bryodulcosigenin 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. Bryodulcosigenin is found in Apis cerana, Bryonia dioica and Siraitia grosvenorii. Bryodulcosigenin was first documented in 2022 (PMID: 34798522). Based on a literature review very few articles have been published on Bryodulcosigenin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201192D          

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     RDKit          3D

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  Mrv1652304282201192D          

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    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  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  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 26  1  0  0  0  0
 22 27  1  6  0  0  0
 19 28  1  6  0  0  0
 15 29  1  6  0  0  0
 14 30  1  1  0  0  0
  8 31  1  1  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
  2 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0052173

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H50O4/c1-18(9-13-24(32)27(4,5)34)19-15-16-28(6)22-12-10-20-21(11-14-23(31)26(20,2)3)30(22,8)25(33)17-29(19,28)7/h10,18-19,21-24,31-32,34H,9,11-17H2,1-8H3/t18-,19-,21-,22+,23+,24-,28+,29-,30+/m1/s1

> <INCHI_KEY>
FPMQKXQOBKDVHF-DJHQPCGUSA-N

> <FORMULA>
C30H50O4

> <MOLECULAR_WEIGHT>
474.726

> <EXACT_MASS>
474.37091009

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
56.70048606046953

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
5.50

> <JCHEM_LOGP>
4.942608173666666

> <ALOGPS_LOGS>
-5.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.32511173348724

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.849642779248693

> <JCHEM_PKA_STRONGEST_BASIC>
-0.870541010658974

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
137.85210000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.23e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,10S,11S,14R,15R)-14-[(2R,5R)-5,6-dihydroxy-6-methylheptan-2-yl]-5-hydroxy-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       0.452  -1.269   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.493  -2.485   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.018  -2.275   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.963  -3.490   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.909  -4.706   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.748  -4.436   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -4.179  -2.545   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -2.599  -0.848   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.558  -2.907   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.355   2.629   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.791  -1.700   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.487  -0.949   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.191   3.252   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.831   3.743   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      13.558   1.312   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4   32   33                                             
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   11   31                                             
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   30                                             
CONECT   15   14    7   16   29                                             
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   14   19                                                  
CONECT   19   18   20   28                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24   25   26                                             
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   23                                                            
CONECT   27   22                                                            
CONECT   28   19                                                            
CONECT   29   15                                                            
CONECT   30   14                                                            
CONECT   31    8                                                            
CONECT   32    3                                                            
CONECT   33    3                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₅₀O₄

Average Mass

474.7260 Da

Monoisotopic Mass

474.37091 Da

IUPAC Name

(1R,2R,5S,10S,11S,14R,15R)-14-[(2R,5R)-5,6-dihydroxy-6-methylheptan-2-yl]-5-hydroxy-1,6,6,11,15-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-7-en-17-one

Traditional Name

(1R,2R,5S,10S,11S,14R,15R)-14-[(2R,5R)-5,6-dihydroxy-6-methylheptan-2-yl]-5-hydroxy-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

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

InChI Identifier

InChI=1S/C30H50O4/c1-18(9-13-24(32)27(4,5)34)19-15-16-28(6)22-12-10-20-21(11-14-23(31)26(20,2)3)30(22,8)25(33)17-29(19,28)7/h10,18-19,21-24,31-32,34H,9,11-17H2,1-8H3/t18-,19-,21-,22+,23+,24-,28+,29-,30+/m1/s1

InChI Key

FPMQKXQOBKDVHF-DJHQPCGUSA-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
Apis cerana	LOTUS Database	35616633
Bryonia dioica	Plant	KNApSAcK
Siraitia grosvenorii	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
24-hydroxysteroid
3-hydroxy-delta-5-steroid
3-hydroxysteroid
14-alpha-methylsteroid
3-beta-hydroxysteroid
3-beta-hydroxy-delta-5-steroid
Oxosteroid
11-oxosteroid
Hydroxysteroid
Delta-5-steroid
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Ketone
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Alcohol
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	5.5	ALOGPS
logP	4.94	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	13.85	ChemAxon
pKa (Strongest Basic)	-0.87	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	137.85 m³·mol⁻¹	ChemAxon
Polarizability	56.7 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00003678

Chemspider ID

354099

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

399493

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li R, Chen C, Liu B, Shi W, Shimizu K, Zhang C: Bryodulcosigenin a natural cucurbitane-type triterpenoid attenuates dextran sulfate sodium (DSS)-induced colitis in mice. Phytomedicine. 2022 Jan;94:153814. doi: 10.1016/j.phymed.2021.153814. Epub 2021 Oct 18. [PubMed:34798522 ]

Showing NP-Card for Bryodulcosigenin (NP0052173)

MOL for NP0052173 (Bryodulcosigenin)

3D MOL for NP0052173 (Bryodulcosigenin)

3D SDF for NP0052173 (Bryodulcosigenin)

3D-SDF for NP0052173 (Bryodulcosigenin)

PDB for NP0052173 (Bryodulcosigenin)

3D PDB for NP0052173 (Bryodulcosigenin)

SMILES for NP0052173 (Bryodulcosigenin)

INCHI for NP0052173 (Bryodulcosigenin)

Structure for NP0052173 (Bryodulcosigenin)

3D Structure for NP0052173 (Bryodulcosigenin)