NP-MRD: Showing NP-Card for (+)-Geranin B (NP0059700)

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Record Information

Version

1.0

Created at

2022-04-28 04:54:51 UTC

Updated at

2022-04-28 04:54:51 UTC

NP-MRD ID

NP0059700

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Geranin B

Description

(1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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 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''. (+)-Geranin B is found in Geranium niveum. Based on a literature review very few articles have been published on (1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282206542D          

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M  END

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M  END


  Mrv1652304282206542D          

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  5  6  2  0  0  0  0
  1  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
  9 11  1  6  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 14 17  1  0  0  0  0
  8 18  1  1  0  0  0
 19  4  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  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
  3 24  1  0  0  0  0
 23 25  1  1  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
 28 31  1  0  0  0  0
 27 32  1  0  0  0  0
 23 33  1  0  0  0  0
 19 33  1  0  0  0  0
 33 34  1  6  0  0  0
 21 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 20 38  1  0  0  0  0
 38 39  1  0  0  0  0
 36 40  1  0  0  0  0
  1 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0059700

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

> <INCHI_IDENTIFIER>
InChI=1S/C30H24O11/c31-14-4-1-12(2-5-14)27-21(37)10-16-18(34)11-23-25(28(16)39-27)26-24-20(36)8-15(32)9-22(24)40-30(41-23,29(26)38)13-3-6-17(33)19(35)7-13/h1-9,11,21,26-27,29,31-38H,10H2/t21-,26+,27+,29-,30-/m0/s1

> <INCHI_KEY>
GVKLXAPXNKDQGB-LQBIBLAPSA-N

> <FORMULA>
C30H24O11

> <MOLECULAR_WEIGHT>
560.511

> <EXACT_MASS>
560.131861593

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
55.51092964015644

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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(20),16,18-hexaene-6,9,17,19,21-pentol

> <ALOGPS_LOGP>
2.61

> <JCHEM_LOGP>
3.8940974183333332

> <ALOGPS_LOGS>
-3.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.172824829777714

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.723400122321127

> <JCHEM_PKA_STRONGEST_BASIC>
-3.28778812469395

> <JCHEM_POLAR_SURFACE_AREA>
189.52999999999997

> <JCHEM_REFRACTIVITY>
142.21540000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.36e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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(20),16,18-hexaene-6,9,17,19,21-pentol

> <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      11.812  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.472  -3.070   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.144  -2.289   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.156  -0.749   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.496   0.010   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.824  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.163  -0.010   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.175   1.530   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.848   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.508   1.550   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      11.859   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.532   4.630   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.544   6.170   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.883   6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.211   6.150   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.199   4.610   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      11.895   8.470   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      14.515   2.289   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.076   0.348   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.536   0.360   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.439  -0.721   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.427  -2.261   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       6.507  -3.358   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.047  -3.370   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.907  -4.776   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.835  -6.005   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.235  -7.423   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.706  -7.612   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.778  -6.383   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.379  -4.965   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.106  -9.031   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       7.163  -8.652   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       7.755  -1.701   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       8.549  -3.020   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       3.954  -0.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.567   1.180   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.665   2.261   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       6.149   1.850   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       7.246   2.931   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       2.083   1.590   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      13.139  -3.090   0.000  0.00  0.00           O+0
CONECT    1    2    6   41                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   24                                                  
CONECT    4    3    5   19                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    5                                                       
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17   14                                                            
CONECT   18    8                                                            
CONECT   19    4   20   33                                                  
CONECT   20   19   21   38                                                  
CONECT   21   20   22   35                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25   33                                             
CONECT   24   23    3                                                       
CONECT   25   23   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29   25                                                       
CONECT   31   28                                                            
CONECT   32   27                                                            
CONECT   33   23   19   34                                                  
CONECT   34   33                                                            
CONECT   35   21   36                                                       
CONECT   36   35   37   40                                                  
CONECT   37   36   38                                                       
CONECT   38   37   20   39                                                  
CONECT   39   38                                                            
CONECT   40   36                                                            
CONECT   41    1                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   94    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₄O₁₁

Average Mass

560.5110 Da

Monoisotopic Mass

560.13186 Da

IUPAC Name

(1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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(20),16,18-hexaene-6,9,17,19,21-pentol

Traditional Name

(1R,5R,6S,13S,21S)-13-(3,4-dihydroxyphenyl)-5-(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(20),16,18-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=C([C@H]1[C@@H]3O)C(O)=CC(O)=C4)C1=CC(O)=C(O)C=C1)C=C2O

InChI Identifier

InChI=1S/C30H24O11/c31-14-4-1-12(2-5-14)27-21(37)10-16-18(34)11-23-25(28(16)39-27)26-24-20(36)8-15(32)9-22(24)40-30(41-23,29(26)38)13-3-6-17(33)19(35)7-13/h1-9,11,21,26-27,29,31-38H,10H2/t21-,26+,27+,29-,30-/m0/s1

InChI Key

GVKLXAPXNKDQGB-LQBIBLAPSA-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
Geranium niveum	Plant	KNApSAcK

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
Proanthocyanidin
Bi- and polyflavonoid skeleton
Catechin
Pyranoflavonoid
Hydroxyflavonoid
Flavan-3-ol
7-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
3'-hydroxyflavonoid
Flavan
Pyranochromene
1-benzopyran
Benzopyran
Chromane
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Ketal
Phenol
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
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	2.61	ALOGPS
logP	3.89	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	8.72	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	189.53 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	142.22 m³·mol⁻¹	ChemAxon
Polarizability	55.51 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

Not Available

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

163038767

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Geranin B (NP0059700)

MOL for NP0059700 ((+)-Geranin B)

3D MOL for NP0059700 ((+)-Geranin B)

3D SDF for NP0059700 ((+)-Geranin B)

3D-SDF for NP0059700 ((+)-Geranin B)

PDB for NP0059700 ((+)-Geranin B)

3D PDB for NP0059700 ((+)-Geranin B)

SMILES for NP0059700 ((+)-Geranin B)

INCHI for NP0059700 ((+)-Geranin B)

Structure for NP0059700 ((+)-Geranin B)

3D Structure for NP0059700 ((+)-Geranin B)