NP-MRD: Showing NP-Card for Rubiprasin B (NP0139780)

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Record Information

Version

2.0

Created at

2022-06-29 20:10:14 UTC

Updated at

2022-06-29 20:10:14 UTC

NP-MRD ID

NP0139780

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rubiprasin B

Description

Rubiprasin B belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Rubiprasin B is found in Rubia cordifolia. Rubiprasin B was first documented in 2018 (PMID: 30593239). Based on a literature review very few articles have been published on Rubiprasin B (PMID: 31343260).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292222102D          

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M  END

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M  END


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    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2732   -1.1265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3977   -0.7392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6882    1.9475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  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 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  1  0  0  0
 13 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  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 15 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
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 27 31  1  0  0  0  0
 24 32  1  1  0  0  0
 21 33  1  6  0  0  0
 20 34  1  1  0  0  0
 15 35  1  1  0  0  0
  8 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0139780

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC(=O)[C@]2(O)[C@@H]4CC(C)(C)CC[C@]4(C)CC[C@@]32C)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C32H52O4/c1-20(33)36-25-11-12-29(7)21(27(25,4)5)10-13-30(8)22(29)18-24(34)32(35)23-19-26(2,3)14-15-28(23,6)16-17-31(30,32)9/h21-23,25,35H,10-19H2,1-9H3/t21-,22+,23+,25-,28+,29-,30+,31-,32+/m0/s1

> <INCHI_KEY>
GWMSDMQWKMSCJR-WWPUQACTSA-N

> <FORMULA>
C32H52O4

> <MOLECULAR_WEIGHT>
500.764

> <EXACT_MASS>
500.386560154

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
88

> <JCHEM_AVERAGE_POLARIZABILITY>
59.94625744948005

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4aR,6aR,6bS,8aR,12aR,12bS,14aR,14bR)-12b-hydroxy-4,4,6a,6b,8a,11,11,14b-octamethyl-13-oxo-docosahydropicen-3-yl acetate

> <ALOGPS_LOGP>
6.09

> <JCHEM_LOGP>
6.6571237896666675

> <ALOGPS_LOGS>
-6.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.233404001355062

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.512744995363438

> <JCHEM_PKA_STRONGEST_BASIC>
-3.886723743501425

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
142.19910000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4aR,6aR,6bS,8aR,12aR,12bS,14aR,14bR)-12b-hydroxy-4,4,6a,6b,8a,11,11,14b-octamethyl-13-oxo-tetradecahydropicen-3-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      13.654  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.424  -0.564   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      15.964  -0.564   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      13.654   0.770   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      12.114   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.344  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.804  -0.564   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.034   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.804   2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.344   2.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.397   3.643   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.650   2.920   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.034   3.437   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.494   3.437   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.414  -1.897   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.414   3.437   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.874   3.437   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.510  -2.103   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.742  -1.380   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334   3.437   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.644  -0.564   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.885   3.635   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       8.264  -0.564   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   16   36                                             
CONECT    9    8   10   13                                                  
CONECT   10    9    5   11   12                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   21   35                                             
CONECT   16   15    8   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   25   34                                             
CONECT   21   20   15   22   33                                             
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   29   32                                             
CONECT   25   24   20   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   30   31                                             
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   27                                                            
CONECT   31   27                                                            
CONECT   32   24                                                            
CONECT   33   21                                                            
CONECT   34   20                                                            
CONECT   35   15                                                            
CONECT   36    8                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₂H₅₂O₄

Average Mass

500.7640 Da

Monoisotopic Mass

500.38656 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC(=O)[C@]2(O)[C@@H]4CC(C)(C)CC[C@]4(C)CC[C@@]32C)C1(C)C

InChI Identifier

InChI=1S/C32H52O4/c1-20(33)36-25-11-12-29(7)21(27(25,4)5)10-13-30(8)22(29)18-24(34)32(35)23-19-26(2,3)14-15-28(23,6)16-17-31(30,32)9/h21-23,25,35H,10-19H2,1-9H3/t21-,22+,23+,25-,28+,29-,30+,31-,32+/m0/s1

InChI Key

GWMSDMQWKMSCJR-WWPUQACTSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Rubia cordifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Tertiary alcohol
Cyclic alcohol
Ketone
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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

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

10217316

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21594133

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wang Z, Zhao SM, Zeng GZ, Tan NH: [Chemical constituents from roots and rhizomes of Rubia oncotricha and their cytotoxic activities]. Zhongguo Zhong Yao Za Zhi. 2018 Nov;43(22):4462-4468. doi: 10.19540/j.cnki.cjcmm.2018.0119. [PubMed:30593239 ]
Quan KT, Min BG, Hwang IH, Choi YJ, Kim SK, Na M: Oleanane triterpenoids from Rubia philippinensis and their inhibitory effect on 20-HETE synthesis. Nat Prod Res. 2021 Apr;35(8):1267-1273. doi: 10.1080/14786419.2019.1645656. Epub 2019 Jul 25. [PubMed:31343260 ]

Showing NP-Card for Rubiprasin B (NP0139780)

MOL for NP0139780 (Rubiprasin B)

3D MOL for NP0139780 (Rubiprasin B)

3D SDF for NP0139780 (Rubiprasin B)

3D-SDF for NP0139780 (Rubiprasin B)

PDB for NP0139780 (Rubiprasin B)

3D PDB for NP0139780 (Rubiprasin B)

SMILES for NP0139780 (Rubiprasin B)

INCHI for NP0139780 (Rubiprasin B)

Structure for NP0139780 (Rubiprasin B)

3D Structure for NP0139780 (Rubiprasin B)