NP-MRD: Showing NP-Card for Symplocosidin (NP0056072)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-28 01:57:17 UTC

Updated at

2022-04-28 01:57:17 UTC

NP-MRD ID

NP0056072

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Symplocosidin

Description

3'-O-methyl-(-)-epicatechin belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol. Symplocosidin is found in Cinnamomum cassia , Cinnamomum obtusifolium, Lindera umbellata var. membranacea and Parapiptadenia rigida. 3'-O-methyl-(-)-epicatechin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 40  0  0  0  0  0  0  0  0999 V2000
    4.8597    2.1530    0.7831 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8642    0.9442    0.0707 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7151    0.2396   -0.2630 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4445    0.6661    0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3012   -0.0316   -0.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0027    0.4965    0.1498 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9694    0.4118   -0.9084 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3234    0.3080   -0.6456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3075    0.9493   -1.3520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6495    0.8185   -1.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6677    1.4514   -1.7492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9634   -0.0014    0.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9761   -0.6743    0.7456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3423   -1.4843    1.7947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6644   -0.5175    0.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5495   -1.1742    1.1353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5053   -0.1049    1.4326 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5661   -0.6131    2.1486 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4725   -1.2053   -0.9554 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7537   -1.6408   -1.3026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8751   -0.9357   -0.9666 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1461   -1.3656   -1.3098 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3322    2.0661    1.7693 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3772    2.9177    0.1288 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9343    2.4101    0.9811 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3895    1.6020    0.6333 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1060    1.6110    0.3219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0304    1.5842   -2.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0207    2.3699   -1.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9946   -0.1497    0.2866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7346   -2.0040    2.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1108   -1.9425    0.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8161   -1.7231    2.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0415    0.6793    2.0306 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7491   -1.5596    1.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6026   -1.7723   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8456   -2.5779   -1.8611 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3355   -2.2007   -1.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 15 13  1  0
 13 14  1  0
 13 12  2  0
 12 10  1  0
 10 11  1  0
 10  9  2  0
 21  3  1  0
 17  6  1  0
  9  8  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
 19 36  1  0
 20 37  1  0
 22 38  1  0
  6 27  1  1
 16 32  1  0
 16 33  1  0
 17 34  1  1
 18 35  1  0
 14 31  1  0
 12 30  1  0
 11 29  1  0
  9 28  1  0
M  END


  Mrv1652309281711142D          

 22 24  0  0  0  0            999 V2000
   -4.2429    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9573   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9573   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2429   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5284   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5284   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0995   -1.0313    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0995   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8839    1.2448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5984    0.8324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5984    0.0074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8839   -0.4052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1695    0.0074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1695    0.8324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6718    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2429   -2.2688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8839    2.0699    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5450    1.2448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850   -1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1695    2.4824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  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  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
  5  8  1  0  0  0  0
  7  6  1  0  0  0  0
 11 12  2  0  0  0  0
 11 16  1  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
  2 17  1  0  0  0  0
  4 18  1  0  0  0  0
 11 19  1  0  0  0  0
 16 20  1  0  0  0  0
  9 21  1  6  0  0  0
 10 13  1  6  0  0  0
 19 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056072

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1O)[C@H]1OC2=C(C[C@H]1O)C(O)=CC(O)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C16H16O6/c1-21-15-4-8(2-3-11(15)18)16-13(20)7-10-12(19)5-9(17)6-14(10)22-16/h2-6,13,16-20H,7H2,1H3/t13-,16-/m1/s1

> <INCHI_KEY>
NJHJXXLBWQXMRO-CZUORRHYSA-N

> <FORMULA>
C16H16O6

> <MOLECULAR_WEIGHT>
304.2946

> <EXACT_MASS>
304.094688244

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
30.37170429077257

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R)-2-(4-hydroxy-3-methoxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <ALOGPS_LOGP>
1.30

> <JCHEM_LOGP>
1.941001071333333

> <ALOGPS_LOGS>
-2.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.980026167284308

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.307243628972142

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2899991857638273

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
78.482

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.25e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
symplocosidin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-SEP-17         0                                  
HETATM    1  C   UNK     0      -7.920   0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.254  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.254  -1.925   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.920  -2.695   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.586  -1.925   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.586  -0.385   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.253   0.385   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -5.253  -2.695   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.919  -1.925   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.919  -0.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.650   2.324   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.984   1.554   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.984   0.014   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.650  -0.756   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.316   0.014   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.316   1.554   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0     -10.587   0.385   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.920  -4.235   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.650   3.864   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.017   2.324   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.585  -2.695   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.316   4.634   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
CONECT    5    4    6    8                                                  
CONECT    6    1    5    7                                                  
CONECT    7   10    6                                                       
CONECT    8    9    5                                                       
CONECT    9    8   10   21                                                  
CONECT   10    9    7   13                                                  
CONECT   11   12   16   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   10                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   11   15   20                                                  
CONECT   17    2                                                            
CONECT   18    4                                                            
CONECT   19   11   22                                                       
CONECT   20   16                                                            
CONECT   21    9                                                            
CONECT   22   19                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
3'-O-Methylepicatechin	HMDB

Chemical Formula

C₁₆H₁₆O₆

Average Mass

304.2946 Da

Monoisotopic Mass

304.09469 Da

IUPAC Name

(2R,3R)-2-(4-hydroxy-3-methoxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

symplocosidin

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1O)[C@H]1OC2=C(C[C@H]1O)C(O)=CC(O)=C2

InChI Identifier

InChI=1S/C16H16O6/c1-21-15-4-8(2-3-11(15)18)16-13(20)7-10-12(19)5-9(17)6-14(10)22-16/h2-6,13,16-20H,7H2,1H3/t13-,16-/m1/s1

InChI Key

NJHJXXLBWQXMRO-CZUORRHYSA-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
Cinnamomum aromaticum	Plant	KNApSAcK
Cinnamomum obtusifolium Nees.	Plant	KNApSAcK
Lindera umbellata var. membranacea	Plant	KNApSAcK
Parapiptadenia rigida	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Catechins

Alternative Parents

Substituents

Catechin
3p-methoxyflavonoid-skeleton
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Chromane
Benzopyran
1-benzopyran
Methoxyphenol
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Ether
Organoheterocyclic compound
Oxacycle
Polyol
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

catechin (CHEBI:70254 )
Flavans, Flavanols and Leucoanthocyanidins (LMPK12020111 )

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	1.3	ALOGPS
logP	1.94	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.31	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	99.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.48 m³·mol⁻¹	ChemAxon
Polarizability	30.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0029175

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029817

KNApSAcK ID

Not Available

Chemspider ID

9595142

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11420256

PDB ID

Not Available

ChEBI ID

70254

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Symplocosidin (NP0056072)

MOL for NP0056072 (Symplocosidin)

3D MOL for NP0056072 (Symplocosidin)

3D SDF for NP0056072 (Symplocosidin)

3D-SDF for NP0056072 (Symplocosidin)

PDB for NP0056072 (Symplocosidin)

3D PDB for NP0056072 (Symplocosidin)

SMILES for NP0056072 (Symplocosidin)

INCHI for NP0056072 (Symplocosidin)

Structure for NP0056072 (Symplocosidin)

3D Structure for NP0056072 (Symplocosidin)