NP-MRD: Showing NP-Card for Pelargoniin C (NP0084327)

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Record Information

Version

2.0

Created at

2022-04-29 05:05:31 UTC

Updated at

2022-04-29 05:05:31 UTC

NP-MRD ID

NP0084327

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pelargoniin C

Description

Pelargoniin C is found in Pelargonium reniforme. Based on a literature review very few articles have been published on (1S,17R,18S,20R,21R)-4,6,7,11,12,21-hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1⁷,¹⁰.0⁴,⁸.0⁹,¹⁴]Docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207052D          

 47 52  0  0  1  0            999 V2000
    2.3208   -4.8203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304292207052D          

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    4.1951   -2.0434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8825   -3.4551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0966   -3.7059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0640   -2.6222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8596   -2.3512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8361   -1.4802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0338   -1.2505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5642   -1.9471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2417   -1.0197    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0118   -0.4053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3283    0.0567    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7918   -0.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3200   -0.7665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6526   -0.0115    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  2  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
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  7 16  1  1  0  0  0
  7 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 11 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 17 22  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  2  0  0  0  0
 24 32  1  0  0  0  0
 23 33  2  0  0  0  0
  5 34  2  0  0  0  0
  2 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  2  0  0  0  0
  4 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 37 41  1  0  0  0  0
 40 42  1  0  0  0  0
 40 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  1  0  0  0  0
 45 46  1  0  0  0  0
 39 46  1  0  0  0  0
 14 46  1  0  0  0  0
 46 47  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084327

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(O)[C@]2([H])OC(=O)C3(O)CC(O)C4(O)OC5=C(C34)C(=CC(O)=C5O)C(=O)O[C@@]1([H])[C@H](OC(=O)C1=CC(O)=C(O)C(O)=C1)O[C@@H]2CO

> <INCHI_IDENTIFIER>
InChI=1S/C26H24O18/c27-5-11-17-16(34)19(23(40-11)43-21(35)6-1-8(28)14(32)9(29)2-6)41-22(36)7-3-10(30)15(33)18-13(7)20-25(38,24(37)42-17)4-12(31)26(20,39)44-18/h1-3,11-12,16-17,19-20,23,27-34,38-39H,4-5H2/t11-,12?,16-,17-,19-,20?,23+,25?,26?/m1/s1

> <INCHI_KEY>
OPDCHSHIPIOYPU-OEHAGQMBSA-N

> <FORMULA>
C26H24O18

> <MOLECULAR_WEIGHT>
624.46

> <EXACT_MASS>
624.096263933

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
55.21864696915573

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,17R,18S,20R,21R)-4,6,7,11,12,21-hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1^{7,10}.0^{4,8}.0^{9,14}]docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoate

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
-1.1439747266666667

> <ALOGPS_LOGS>
-1.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.656991878727217

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.94905320116985

> <JCHEM_PKA_STRONGEST_BASIC>
-3.70900400770594

> <JCHEM_POLAR_SURFACE_AREA>
299.66

> <JCHEM_REFRACTIVITY>
133.6382

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,17R,18S,20R,21R)-4,6,7,11,12,21-hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1^{7,10}.0^{4,8}.0^{9,14}]docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoate

> <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  O   UNK     0       4.332  -8.998   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.660  -7.493   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.144  -7.019   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.496  -5.487   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.054  -5.338   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.461  -5.989   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      10.631  -4.956   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.968  -3.553   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0       9.127  -4.843   0.000  0.00  0.00           H+0
HETATM   10  O   UNK     0       8.429  -3.512   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      10.708  -2.181   0.000  0.00  0.00           C+0
HETATM   12  H   UNK     0      11.189  -0.718   0.000  0.00  0.00           H+0
HETATM   13  O   UNK     0       9.364  -1.331   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.773  -1.337   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.724   0.202   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      11.169  -6.399   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0      12.175  -4.970   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.031  -3.664   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      12.293  -2.294   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.129  -1.001   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.667  -1.078   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      12.901  -6.328   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      14.441  -6.379   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.166  -7.737   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.706  -7.787   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      17.432  -9.146   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      18.971  -9.196   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      16.618 -10.453   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      17.344 -11.811   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      15.079 -10.403   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      14.266 -11.711   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      14.353  -9.045   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      15.254  -5.071   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       7.831  -3.814   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       3.514  -6.450   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       2.047  -6.918   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       3.853  -4.895   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.338  -4.389   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       5.294  -2.763   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.796  -2.334   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       2.920  -3.635   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       2.318  -1.903   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       3.755  -0.757   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       2.479   0.106   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       5.211  -0.215   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       6.197  -1.431   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0       6.818  -0.022   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   38                                                  
CONECT    5    4    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   16   17                                             
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8   12   13   19                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   46                                                  
CONECT   15   14                                                            
CONECT   16    7                                                            
CONECT   17    7   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   11   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   17   23                                                       
CONECT   23   22   24   33                                                  
CONECT   24   23   25   32                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   24                                                       
CONECT   33   23                                                            
CONECT   34    5                                                            
CONECT   35    2   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   41                                                  
CONECT   38   37    4   39                                                  
CONECT   39   38   40   46                                                  
CONECT   40   39   41   42   43                                             
CONECT   41   40   37                                                       
CONECT   42   40                                                            
CONECT   43   40   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46                                                       
CONECT   46   45   39   14   47                                             
CONECT   47   46                                                            
MASTER        0    0    0    0    0    0    0    0   47    0  104    0
END

View in JSmol

Synonyms

Value	Source
(1S,17R,18S,20R,21R)-4,6,7,11,12,21-Hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1,.0,.0,]docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoic acid	Generator

Chemical Formula

C₂₆H₂₄O₁₈

Average Mass

624.4600 Da

Monoisotopic Mass

624.09626 Da

IUPAC Name

(1S,17R,18S,20R,21R)-4,6,7,11,12,21-hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1^{7,10}.0^{4,8}.0^{9,14}]docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoate

Traditional Name

(1S,17R,18S,20R,21R)-4,6,7,11,12,21-hexahydroxy-20-(hydroxymethyl)-3,15-dioxo-2,16,19,22-tetraoxapentacyclo[15.3.1.1^{7,10}.0^{4,8}.0^{9,14}]docosa-9,11,13-trien-18-yl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)[C@]2([H])OC(=O)C3(O)CC(O)C4(O)OC5=C(C34)C(=CC(O)=C5O)C(=O)O[C@@]1([H])[C@H](OC(=O)C1=CC(O)=C(O)C(O)=C1)O[C@@H]2CO

InChI Identifier

InChI=1S/C26H24O18/c27-5-11-17-16(34)19(23(40-11)43-21(35)6-1-8(28)14(32)9(29)2-6)41-22(36)7-3-10(30)15(33)18-13(7)20-25(38,24(37)42-17)4-12(31)26(20,39)44-18/h1-3,11-12,16-17,19-20,23,27-34,38-39H,4-5H2/t11-,12?,16-,17-,19-,20?,23+,25?,26?/m1/s1

InChI Key

OPDCHSHIPIOYPU-OEHAGQMBSA-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
Pelargonium reniforme	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	0.21	ALOGPS
logP	-1.1	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	7.95	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	299.66 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	133.64 m³·mol⁻¹	ChemAxon
Polarizability	55.22 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	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

C00053642

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163191612

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pelargoniin C (NP0084327)

MOL for NP0084327 (Pelargoniin C)

3D MOL for NP0084327 (Pelargoniin C)

3D SDF for NP0084327 (Pelargoniin C)

3D-SDF for NP0084327 (Pelargoniin C)

PDB for NP0084327 (Pelargoniin C)

3D PDB for NP0084327 (Pelargoniin C)

SMILES for NP0084327 (Pelargoniin C)

INCHI for NP0084327 (Pelargoniin C)

Structure for NP0084327 (Pelargoniin C)

3D Structure for NP0084327 (Pelargoniin C)