NP-MRD: Showing NP-Card for Norbergenin (NP0073099)

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Record Information

Version

2.0

Created at

2022-04-28 18:21:46 UTC

Updated at

2022-04-28 18:21:46 UTC

NP-MRD ID

NP0073099

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Norbergenin

Description

(2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0²,⁷]Tetradeca-1(14),10,12-trien-9-one belongs to the class of organic compounds known as gallic acid and derivatives. Gallic acid and derivatives are compounds containing a 3,4,5-trihydroxybenzoic acid moiety. Norbergenin is found in Ardisia colorata, Ardisia crenata , Lotus corniculatus, Peltophorum africanum, Saxifraga stolonifera, Saxifraga stolonifera Meerb. and Woodfordia fruticosa . Based on a literature review very few articles have been published on (2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0²,⁷]Tetradeca-1(14),10,12-trien-9-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
    2.2388   -2.7323   -2.2277 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4254   -1.8299   -1.9027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0900   -1.8530   -2.2701 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8875   -1.0871   -1.5574 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3750    0.2425   -1.1538 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1103    0.8470   -0.1428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3557    0.2785    0.0699 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0559    1.1085    1.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3138    0.6417    1.4229 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1180   -1.1223    0.6187 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2914   -0.9805    1.7399 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3454   -1.9400   -0.3978 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2504   -2.5805    0.1527 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0408    0.2882   -0.7369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8990   -0.7082   -1.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2207   -0.6189   -0.6946 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6736    0.4363    0.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9905    0.5399    0.4825 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7939    1.4544    0.4404 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2688    2.5091    1.2049 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4902    1.3705    0.0373 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5382    2.3237    0.3549 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7490   -0.9740   -2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4510    0.9242   -2.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9121    0.2497   -0.8821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3928    1.1526    2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1199    2.1461    0.7310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9748    1.1854    0.9211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0633   -1.5762    0.9179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7144   -1.3487    2.5627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0394   -2.7053   -0.7991 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1373   -1.9557    0.8389 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8887   -1.4091   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2857    1.3261    1.0363 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7171    3.2838    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8216    3.1135    0.9079 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 17 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 14  2  0
  4 12  1  0
 12 13  1  0
 12 10  1  0
 10 11  1  0
 10  7  1  0
 14  5  1  0
 14 15  1  0
  9 28  1  0
  8 26  1  0
  8 27  1  0
  7 25  1  6
  5 24  1  6
  4 23  1  6
 16 33  1  0
 18 34  1  0
 20 35  1  0
 22 36  1  0
 12 31  1  6
 13 32  1  0
 10 29  1  1
 11 30  1  0
M  END


  Mrv1652304282220212D          

 22 24  0  0  1  0            999 V2000
    3.6020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1270   -0.3020    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5395   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1105    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8395    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
  9 13  1  0  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  1  0  0  0
 15 17  1  1  0  0  0
 17 18  1  0  0  0  0
 14 19  1  1  0  0  0
 13 20  1  1  0  0  0
  2 21  1  0  0  0  0
  1 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0073099

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H]2[C@@H](OC(=O)C3=CC(O)=C(O)C(O)=C23)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C13H14O9/c14-2-5-8(17)10(19)12-11(21-5)6-3(13(20)22-12)1-4(15)7(16)9(6)18/h1,5,8,10-12,14-19H,2H2/t5-,8+,10+,11+,12+/m1/s1

> <INCHI_KEY>
GDYGAIKPBLFCKR-VPOXOROISA-N

> <FORMULA>
C13H14O9

> <MOLECULAR_WEIGHT>
314.246

> <EXACT_MASS>
314.063782031

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.48043674826817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(14),10,12-trien-9-one

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-1.3727170213333333

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.162207017552142

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.825597215003298

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9791924012295246

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
68.883

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(14),10,12-trien-9-one

> <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       6.724   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.414   3.437   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.874  -1.897   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.184  -3.231   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.104   2.104   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.206   3.437   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.746   3.437   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.746   0.770   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -0.206  -1.897   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       9.034   0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       7.494   3.437   0.000  0.00  0.00           O+0
CONECT    1    2    6   22                                                  
CONECT    2    1    3   21                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   16                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13    9   14   20                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15    8                                                       
CONECT   17   15   18                                                       
CONECT   18   17                                                            
CONECT   19   14                                                            
CONECT   20   13                                                            
CONECT   21    2                                                            
CONECT   22    1                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₄O₉

Average Mass

314.2460 Da

Monoisotopic Mass

314.06378 Da

IUPAC Name

(2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(14),10,12-trien-9-one

Traditional Name

(2S,4R,5R,6S,7S)-5,6,12,13,14-pentahydroxy-4-(hydroxymethyl)-3,8-dioxatricyclo[8.4.0.0^{2,7}]tetradeca-1(14),10,12-trien-9-one

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H]2[C@@H](OC(=O)C3=CC(O)=C(O)C(O)=C23)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C13H14O9/c14-2-5-8(17)10(19)12-11(21-5)6-3(13(20)22-12)1-4(15)7(16)9(6)18/h1,5,8,10-12,14-19H,2H2/t5-,8+,10+,11+,12+/m1/s1

InChI Key

GDYGAIKPBLFCKR-VPOXOROISA-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
Ardisia colorata	Plant	KNApSAcK
Ardisia crenata	Plant	KNApSAcK
Lotus corniculatus	LOTUS Database	35616633
Peltophorum africanum	LOTUS Database	35616633
Saxifraga stolonifera	LOTUS Database	35616633
Saxifraga stolonifera Meerb.	Plant	KNApSAcK
Woodfordia fruticosa	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gallic acid and derivatives. Gallic acid and derivatives are compounds containing a 3,4,5-trihydroxybenzoic acid moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Gallic acid and derivatives

Alternative Parents

Substituents

Gallic acid or derivatives
2-benzopyran
Isochromane
Benzopyran
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Oxane
Monosaccharide
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
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	-1.1	ALOGPS
logP	-1.4	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Acidic)	7.83	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.91 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	68.88 m³·mol⁻¹	ChemAxon
Polarizability	27.48 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	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

158227268

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Norbergenin (NP0073099)

MOL for NP0073099 (Norbergenin)

3D MOL for NP0073099 (Norbergenin)

3D SDF for NP0073099 (Norbergenin)

3D-SDF for NP0073099 (Norbergenin)

PDB for NP0073099 (Norbergenin)

3D PDB for NP0073099 (Norbergenin)

SMILES for NP0073099 (Norbergenin)

INCHI for NP0073099 (Norbergenin)

Structure for NP0073099 (Norbergenin)

3D Structure for NP0073099 (Norbergenin)