NP-MRD: Showing NP-Card for polacandrin (NP0266501)

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Record Information

Version

2.0

Created at

2022-09-08 10:51:39 UTC

Updated at

2022-09-08 10:51:39 UTC

NP-MRD ID

NP0266501

Secondary Accession Numbers

None

Natural Product Identification

Common Name

polacandrin

Description

Polacandrin belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton. polacandrin is found in Polanisia dodecandra. polacandrin was first documented in 2003 (PMID: 14695802). Based on a literature review very few articles have been published on Polacandrin (PMID: 20381821).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082212512D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309082212512D          

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    1.2487   -2.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9960   -2.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7119   -1.6225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7094   -1.9828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5278   -3.0277    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3399   -2.8825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2475   -3.8037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4354   -3.9489    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1551   -4.7248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4586   -3.8067    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
  2  4  1  0  0  0  0
  5  2  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  1  0  0  0
  8 10  1  6  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 15 13  1  6  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 19 18  1  1  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 19 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  1  1  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 20 33  1  0  0  0  0
 33 34  1  1  0  0  0
  8 35  1  0  0  0  0
  5 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0266501

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(O)[C@@H]1CC[C@](C)(O1)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@H]1[C@@]2(C)CC[C@H]2C(C)(C)[C@H](O)C[C@@H](O)[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C30H52O5/c1-25(2)19-10-13-27(5)20(30(19,8)22(33)16-21(25)32)15-18(31)24-17(9-12-28(24,27)6)29(7)14-11-23(35-29)26(3,4)34/h17-24,31-34H,9-16H2,1-8H3/t17-,18+,19-,20-,21+,22+,23-,24-,27+,28+,29-,30-/m0/s1

> <INCHI_KEY>
ZDMWPLUKUXQVLI-QXTFULOPSA-N

> <FORMULA>
C30H52O5

> <MOLECULAR_WEIGHT>
492.741

> <EXACT_MASS>
492.381474774

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
57.773750710128

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,3R,5R,7S,10R,11R,14S,15R,16R)-14-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-3,5,16-triol

> <JCHEM_LOGP>
3.2495974936666654

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.439120498063208

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.96680247350227

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8389624674486305

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
137.54529999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3R,5R,7S,10R,11R,14S,15R,16R)-14-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-3,5,16-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -6.852  -6.489   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.466  -7.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.795  -5.775   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -6.138  -8.546   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -4.081  -7.832   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.810  -9.348   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.284  -9.559   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.612  -8.173   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.304  -8.986   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.667  -6.957   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.095  -5.478   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.179  -4.614   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.395  -5.559   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.764  -4.064   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.872  -7.007   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.865  -8.184   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.342  -9.633   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.381  -7.913   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.904  -6.465   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.420  -6.194   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.897  -7.642   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.943  -4.746   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.950  -3.568   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.434  -3.839   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.911  -5.288   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.331  -3.861   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.459  -4.474   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.929  -3.029   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.791  -3.701   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.452  -5.652   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.968  -5.381   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.929  -7.100   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.413  -7.371   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.889  -8.820   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -2.723  -7.106   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6   35                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   35                                             
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   25                                             
CONECT   14   13                                                            
CONECT   15   13   10   16                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21   22   33                                             
CONECT   21   20                                                            
CONECT   22   20   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   19   13   26                                             
CONECT   26   25                                                            
CONECT   27   22   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   20   34                                                  
CONECT   34   33                                                            
CONECT   35    8    5                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₅₂O₅

Average Mass

492.7410 Da

Monoisotopic Mass

492.38147 Da

IUPAC Name

(1S,2R,3R,5R,7S,10R,11R,14S,15R,16R)-14-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-3,5,16-triol

Traditional Name

(1S,2R,3R,5R,7S,10R,11R,14S,15R,16R)-14-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-3,5,16-triol

CAS Registry Number

Not Available

SMILES

CC(C)(O)[C@@H]1CC[C@](C)(O1)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@H]1[C@@]2(C)CC[C@H]2C(C)(C)[C@H](O)C[C@@H](O)[C@]12C

InChI Identifier

InChI=1S/C30H52O5/c1-25(2)19-10-13-27(5)20(30(19,8)22(33)16-21(25)32)15-18(31)24-17(9-12-28(24,27)6)29(7)14-11-23(35-29)26(3,4)34/h17-24,31-34H,9-16H2,1-8H3/t17-,18+,19-,20-,21+,22+,23-,24-,27+,28+,29-,30-/m0/s1

InChI Key

ZDMWPLUKUXQVLI-QXTFULOPSA-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
Polanisia dodecandra	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpene saponins. These are glycosylated derivatives of triterpene sapogenins. The sapogenin moiety backbone is usually based on the oleanane, ursane, taraxastane, bauerane, lanostane, lupeol, lupane, dammarane, cycloartane, friedelane, hopane, 9b,19-cyclo-lanostane, cycloartane, or cycloartanol skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Triterpene saponins

Alternative Parents

Substituents

Triterpene saponin
Triterpenoid
3-hydroxysteroid
14-alpha-methylsteroid
1-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
3-alpha-hydroxysteroid
Steroid
Tetrahydrofuran
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Polyol
Oxacycle
Ether
Dialkyl ether
Organoheterocyclic compound
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

triterpenoid saponin (CHEBI:66768 )

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	3.25	ChemAxon
pKa (Strongest Acidic)	13.97	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	137.55 m³·mol⁻¹	ChemAxon
Polarizability	57.77 Å³	ChemAxon
Number of Rings	5	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

C00044411

Chemspider ID

24695491

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44584607

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Asai T, Hara N, Fujimoto Y: Fatty acid derivatives and dammarane triterpenes from the glandular trichome exudates of Ibicella lutea and Proboscidea louisiana. Phytochemistry. 2010 Jun;71(8-9):877-94. doi: 10.1016/j.phytochem.2010.02.013. Epub 2010 Apr 8. [PubMed:20381821 ]
Simirgiotis MJ, Jimenez C, Rodriguez J, Giordano OS, Tonn CE: New dammarane triterpenes from the aerial parts of Ibicella lutea grown in Argentina. J Nat Prod. 2003 Dec;66(12):1586-92. doi: 10.1021/np030273i. [PubMed:14695802 ]
LOTUS database [Link]

Showing NP-Card for polacandrin (NP0266501)

MOL for NP0266501 (polacandrin)

3D MOL for NP0266501 (polacandrin)

3D SDF for NP0266501 (polacandrin)

3D-SDF for NP0266501 (polacandrin)

PDB for NP0266501 (polacandrin)

3D PDB for NP0266501 (polacandrin)

SMILES for NP0266501 (polacandrin)

INCHI for NP0266501 (polacandrin)

Structure for NP0266501 (polacandrin)

3D Structure for NP0266501 (polacandrin)