NP-MRD: Showing NP-Card for Pomegralignan (NP0084355)

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Record Information

Version

2.0

Created at

2022-04-29 05:06:32 UTC

Updated at

2022-04-29 05:06:32 UTC

NP-MRD ID

NP0084355

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pomegralignan

Description

Pomegralignan belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. Pomegralignan is found in Punica granatum . Pomegralignan was first documented in 2014 (PMID: 24444944). Based on a literature review very few articles have been published on Pomegralignan.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207062D          

 37 40  0  0  1  0            999 V2000
    7.0714    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3569    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6424    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6424   -0.1271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3569   -0.5396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9279   -0.5396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9279   -1.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135   -0.1271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4990   -0.5396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4990    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -1.2054   -0.1006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0030    2.2580    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.9279    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
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  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
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 13 14  2  0  0  0  0
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 19 20  1  6  0  0  0
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 21 22  2  0  0  0  0
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 23 24  1  0  0  0  0
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 10 37  1  0  0  0  0
  3 37  1  0  0  0  0
M  END

     RDKit          3D

 64 67  0  0  0  0  0  0  0  0999 V2000
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   -0.7738    0.5265   -0.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8302   -0.2569    0.3832 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0756   -0.7441    0.9619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0523   -1.4556    1.9979 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3197   -0.4643    0.4262 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5303   -0.9530    1.0105 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.1389   -1.8198    0.1310 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0109   -1.2153   -0.7521 C   0  0  2  0  0  0  0  0  0  0  0  0
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  6  7  1  0
  7  8  1  0
  8 29  2  0
 29 28  1  0
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  6  5  1  0
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  3 35  2  0
 35 36  1  0
 35 34  1  0
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 30  6  1  0
 33  5  1  0
  9  8  1  0
 26 17  1  0
  6 41  1  1
 28 57  1  0
 12 45  1  0
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M  END


  Mrv1652304292207062D          

 37 40  0  0  1  0            999 V2000
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    4.2135    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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 15 31  2  0  0  0  0
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 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
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 32 35  2  0  0  0  0
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 10 37  1  0  0  0  0
  3 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084355

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(OC2=C(C=C(C=C2OC)C(=O)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1CO)C1=CC(OC)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O12/c1-32-15-6-10(3-4-14(15)27)21-13(8-25)12-5-11(7-16(33-2)22(12)35-21)23(31)36-24-20(30)19(29)18(28)17(9-26)34-24/h3-7,13,17-21,24-30H,8-9H2,1-2H3/t13-,17+,18+,19-,20+,21+,24-/m0/s1

> <INCHI_KEY>
DRSIREWMODXMBU-WTJKROCISA-N

> <FORMULA>
C24H28O12

> <MOLECULAR_WEIGHT>
508.476

> <EXACT_MASS>
508.158076342

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
50.53311080267588

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2S,3R)-2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydro-1-benzofuran-5-carboxylate

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
-0.4198388576666664

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.197255897559298

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.907728588815768

> <JCHEM_PKA_STRONGEST_BASIC>
-2.729833530041825

> <JCHEM_POLAR_SURFACE_AREA>
184.59999999999997

> <JCHEM_REFRACTIVITY>
121.00979999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2S,3R)-2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydro-1-benzofuran-5-carboxylate

> <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      13.200   1.303   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      11.866   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.533   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.533  -0.237   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      11.866  -1.007   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       9.199  -1.007   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.199  -2.547   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.865  -0.237   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.531  -1.007   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.865   1.303   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       6.531   2.073   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.198   1.303   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.744   0.132   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.250  -0.188   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM   20  H   UNK     0      -1.872   4.215   0.000  0.00  0.00           H+0
HETATM   21  C   UNK     0      -2.713   2.843   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.483   1.509   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.023   1.509   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -5.793   0.175   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -5.023  -1.158   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -5.793   2.843   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -7.333   2.843   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -5.023   4.177   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.483   4.177   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.268   4.089   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       3.864   6.693   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.198  -0.237   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       9.199   2.073   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   37                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   36                                                  
CONECT   13   12   14   35                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   31                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21   30                                             
CONECT   20   19                                                            
CONECT   21   19   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   21                                                       
CONECT   30   19   31                                                       
CONECT   31   15   30   32                                                  
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   13                                                       
CONECT   36   12                                                            
CONECT   37   10    3                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₈O₁₂

Average Mass

508.4760 Da

Monoisotopic Mass

508.15808 Da

IUPAC Name

(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2S,3R)-2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydro-1-benzofuran-5-carboxylate

Traditional Name

(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl (2S,3R)-2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydro-1-benzofuran-5-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(OC2=C(C=C(C=C2OC)C(=O)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1CO)C1=CC(OC)=C(O)C=C1

InChI Identifier

InChI=1S/C24H28O12/c1-32-15-6-10(3-4-14(15)27)21-13(8-25)12-5-11(7-16(33-2)22(12)35-21)23(31)36-24-20(30)19(29)18(28)17(9-26)34-24/h3-7,13,17-21,24-30H,8-9H2,1-2H3/t13-,17+,18+,19-,20+,21+,24-/m0/s1

InChI Key

DRSIREWMODXMBU-WTJKROCISA-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
Punica granatum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

2-arylbenzofuran flavonoid
Hydrolyzable tannin
Neolignan skeleton
Hexose monosaccharide
M-methoxybenzoic acid or derivatives
Methoxyphenol
Coumaran
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Acetal
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	0.21	ALOGPS
logP	-0.42	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	9.91	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	184.6 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	121.01 m³·mol⁻¹	ChemAxon
Polarizability	50.53 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00053697

Chemspider ID

108341303

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102502690

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ito H, Li P, Koreishi M, Nagatomo A, Nishida N, Yoshida T: Ellagitannin oligomers and a neolignan from pomegranate arils and their inhibitory effects on the formation of advanced glycation end products. Food Chem. 2014;152:323-30. doi: 10.1016/j.foodchem.2013.11.160. Epub 2013 Dec 4. [PubMed:24444944 ]

Showing NP-Card for Pomegralignan (NP0084355)

MOL for NP0084355 (Pomegralignan)

3D MOL for NP0084355 (Pomegralignan)

3D SDF for NP0084355 (Pomegralignan)

3D-SDF for NP0084355 (Pomegralignan)

PDB for NP0084355 (Pomegralignan)

3D PDB for NP0084355 (Pomegralignan)

SMILES for NP0084355 (Pomegralignan)

INCHI for NP0084355 (Pomegralignan)

Structure for NP0084355 (Pomegralignan)

3D Structure for NP0084355 (Pomegralignan)