NP-MRD: Showing NP-Card for (1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol (NP0330338)

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Record Information

Version

1.0

Created at

2022-09-12 15:35:14 UTC

Updated at

2022-09-12 15:35:14 UTC

NP-MRD ID

NP0330338

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol

Description

GERANIN A belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''. (1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol is found in Prunus armeniaca. Based on a literature review very few articles have been published on GERANIN A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122217352D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122217352D          

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  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
 15 14  1  1  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 16 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 26 32  1  0  0  0  0
 25 33  1  0  0  0  0
 13 33  1  0  0  0  0
 25 34  1  0  0  0  0
 15 34  1  0  0  0  0
 34 35  1  6  0  0  0
  9 36  1  0  0  0  0
 36 37  1  0  0  0  0
  6 37  1  0  0  0  0
 37 38  1  1  0  0  0
  5 39  1  0  0  0  0
 39 40  2  0  0  0  0
  2 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330338

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O[C@@H]1C1=CC=C(O)C=C1)C1=C(O[C@]3(OC4=CC(O)=CC(O)=C4[C@@H]1[C@@H]3O)C1=CC=C(O)C=C1)C=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C30H24O10/c31-15-5-1-13(2-6-15)27-21(36)11-18-19(34)12-23-25(28(18)38-27)26-24-20(35)9-17(33)10-22(24)39-30(40-23,29(26)37)14-3-7-16(32)8-4-14/h1-10,12,21,26-27,29,31-37H,11H2/t21-,26-,27+,29-,30+/m0/s1

> <INCHI_KEY>
LQRHGTVFFPMWCG-VCFSXNJSSA-N

> <FORMULA>
C30H24O10

> <MOLECULAR_WEIGHT>
544.512

> <EXACT_MASS>
544.136946973

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
54.80845477615178

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,5R,6S,13R,21S)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{15,20}]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol

> <JCHEM_LOGP>
4.19766274

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.257798545162297

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.822574859192049

> <JCHEM_PKA_STRONGEST_BASIC>
-3.287788032460389

> <JCHEM_POLAR_SURFACE_AREA>
169.29999999999998

> <JCHEM_REFRACTIVITY>
140.2345

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,5R,6S,13R,21S)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{15,20}]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0      11.895   8.470   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      11.883   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.211   6.150   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.199   4.610   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.859   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.848   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      10.508   1.550   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.496   0.010   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.824  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.812  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      13.139  -3.090   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      10.472  -3.070   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.144  -2.289   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.156  -0.749   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.076   0.348   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.536   0.360   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.149   1.850   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.246   2.931   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.665   2.261   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.567   1.180   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.083   1.590   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       3.954  -0.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.439  -0.721   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.427  -2.261   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.507  -3.358   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.907  -4.776   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.835  -6.005   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.235  -7.423   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.706  -7.612   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.106  -9.031   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.778  -6.383   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.379  -4.965   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.047  -3.370   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       7.755  -1.701   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       8.549  -3.020   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      13.163  -0.010   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      13.175   1.530   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      14.515   2.289   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      10.532   4.630   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      10.544   6.170   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   40                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   39                                                  
CONECT    6    5    7   37                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   36                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   33                                                  
CONECT   14   13    8   15                                                  
CONECT   15   14   16   34                                                  
CONECT   16   15   17   23                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   16   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   33   34                                             
CONECT   26   25   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   26                                                       
CONECT   33   25   13                                                       
CONECT   34   25   15   35                                                  
CONECT   35   34                                                            
CONECT   36    9   37                                                       
CONECT   37   36    6   38                                                  
CONECT   38   37                                                            
CONECT   39    5   40                                                       
CONECT   40   39    2                                                       
MASTER        0    0    0    0    0    0    0    0   40    0   92    0
END

View in JSmol

Synonyms

Value	Source
Epi-afzelechin-(4-8,2-O-7)afzelechin	MeSH

Chemical Formula

C₃₀H₂₄O₁₀

Average Mass

544.5120 Da

Monoisotopic Mass

544.13695 Da

IUPAC Name

(1S,5R,6S,13R,21S)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{15,20}]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol

Traditional Name

(1S,5R,6S,13R,21S)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0^{2,11}.0^{3,8}.0^{15,20}]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol

CAS Registry Number

Not Available

SMILES

O[C@H]1CC2=C(O[C@@H]1C1=CC=C(O)C=C1)C1=C(O[C@]3(OC4=CC(O)=CC(O)=C4[C@@H]1[C@@H]3O)C1=CC=C(O)C=C1)C=C2O

InChI Identifier

InChI=1S/C30H24O10/c31-15-5-1-13(2-6-15)27-21(36)11-18-19(34)12-23-25(28(18)38-27)26-24-20(35)9-17(33)10-22(24)39-30(40-23,29(26)37)14-3-7-16(32)8-4-14/h1-10,12,21,26-27,29,31-37H,11H2/t21-,26-,27+,29-,30+/m0/s1

InChI Key

LQRHGTVFFPMWCG-VCFSXNJSSA-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
Prunus armeniaca	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Biflavonoids and polyflavonoids

Direct Parent

Biflavonoids and polyflavonoids

Alternative Parents

Substituents

A-type proanthocyanidin
Bi- and polyflavonoid skeleton
Proanthocyanidin
Pyranoflavonoid
Flavan-3-ol
3-hydroxyflavonoid
Hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavan
Pyranochromene
Benzopyran
1-benzopyran
Chromane
Phenol
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Ketal
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Ether
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	4.2	ChemAxon
pKa (Strongest Acidic)	8.82	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	169.3 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	140.23 m³·mol⁻¹	ChemAxon
Polarizability	54.81 Å³	ChemAxon
Number of Rings	7	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

C00013277

Chemspider ID

4475976

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5317050

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol (NP0330338)

MOL for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

3D MOL for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

3D SDF for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

3D-SDF for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

PDB for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

3D PDB for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

SMILES for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

INCHI for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

Structure for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)

3D Structure for NP0330338 ((1s,5r,6s,13r,21s)-5,13-bis(4-hydroxyphenyl)-4,12,14-trioxapentacyclo[11.7.1.0²,¹¹.0³,⁸.0¹⁵,²⁰]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol)