NP-MRD: Showing NP-Card for 6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol (NP0218406)

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Record Information

Version

2.0

Created at

2022-09-05 19:03:59 UTC

Updated at

2022-09-05 19:03:59 UTC

NP-MRD ID

NP0218406

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol

Description

SAUCERNEOL H belongs to the class of organic compounds known as dibenzylbutane lignans. These are lignan compounds containing a 2,3-dibenzylbutane moiety. 6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol is found in Saururus chinensis. 6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol was first documented in 2008 (PMID: 18841903). Based on a literature review a small amount of articles have been published on SAUCERNEOL H (PMID: 19898804).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052221042D          

 26 29  0  0  1  0            999 V2000
    5.4957    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2102    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3536    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3536    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9667    3.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6311    4.4787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8106    4.3924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7812    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0668    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  6 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  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  2  0  0  0  0
 18 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 21 26  1  0  0  0  0
M  END


  Mrv1652309052221042D          

 26 29  0  0  1  0            999 V2000
    5.4957    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2102    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3536    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3536    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6391    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9667    3.7250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6311    4.4787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8106    4.3924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7812    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0668    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  6 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  1  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  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  2  0  0  0  0
 18 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 21 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0218406

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC1=CC2=C(OCO2)C=C1O)[C@@H](C)[C@H](O)C1=CC=C2OCOC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H22O6/c1-11(5-14-7-18-19(8-15(14)21)26-10-25-18)12(2)20(22)13-3-4-16-17(6-13)24-9-23-16/h3-4,6-8,11-12,20-22H,5,9-10H2,1-2H3/t11-,12-,20+/m1/s1

> <INCHI_KEY>
MUMFFBHTQFUOMR-HTGLOVNISA-N

> <FORMULA>
C20H22O6

> <MOLECULAR_WEIGHT>
358.39

> <EXACT_MASS>
358.141638428

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
37.78174704412356

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-[(2R,3R,4S)-4-(2H-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2H-1,3-benzodioxol-5-ol

> <JCHEM_LOGP>
3.762828307333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.1651287042027

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.024166685616587

> <JCHEM_PKA_STRONGEST_BASIC>
-3.163987592899484

> <JCHEM_POLAR_SURFACE_AREA>
77.38000000000001

> <JCHEM_REFRACTIVITY>
93.6486

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(2R,3R,4S)-4-(2H-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2H-1,3-benzodioxol-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      10.259   5.923   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.259   4.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.592   3.613   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.926   4.383   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.926   5.923   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.260   6.693   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.593   5.923   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.593   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.260   3.613   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      14.260   2.073   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      16.738   6.953   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      16.111   8.360   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      14.580   8.199   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.925   3.613   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.925   2.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.591   5.923   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.126   4.089   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.126   1.597   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   13                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9                                                            
CONECT   11    7   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    6                                                       
CONECT   14    2   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₂O₆

Average Mass

358.3900 Da

Monoisotopic Mass

358.14164 Da

IUPAC Name

6-[(2R,3R,4S)-4-(2H-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2H-1,3-benzodioxol-5-ol

Traditional Name

6-[(2R,3R,4S)-4-(2H-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2H-1,3-benzodioxol-5-ol

CAS Registry Number

Not Available

SMILES

C[C@H](CC1=CC2=C(OCO2)C=C1O)[C@@H](C)[C@H](O)C1=CC=C2OCOC2=C1

InChI Identifier

InChI=1S/C20H22O6/c1-11(5-14-7-18-19(8-15(14)21)26-10-25-18)12(2)20(22)13-3-4-16-17(6-13)24-9-23-16/h3-4,6-8,11-12,20-22H,5,9-10H2,1-2H3/t11-,12-,20+/m1/s1

InChI Key

MUMFFBHTQFUOMR-HTGLOVNISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Saururus chinensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dibenzylbutane lignans. These are lignan compounds containing a 2,3-dibenzylbutane moiety.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Dibenzylbutane lignans

Sub Class

Not Available

Direct Parent

Dibenzylbutane lignans

Alternative Parents

Substituents

Dibenzylbutane lignan skeleton
Benzodioxole
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Acetal
Organic oxygen compound
Hydrocarbon derivative
Aromatic 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	3.76	ChemAxon
pKa (Strongest Acidic)	10.02	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	77.38 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	93.65 m³·mol⁻¹	ChemAxon
Polarizability	37.78 Å³	ChemAxon
Number of Rings	4	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00040227

Chemspider ID

24700956

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44580017

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lee YK, Seo CS, Lee CS, Lee KS, Kang SJ, Jahng Y, Chang HW, Son JK: Inhibition of DNA topoisomerases I and II and cytotoxicity by lignans from Saururus chinensis. Arch Pharm Res. 2009 Oct;32(10):1409-15. doi: 10.1007/s12272-009-2010-7. Epub 2009 Nov 8. [PubMed:19898804 ]
Seo CS, Zheng MS, Woo MH, Lee CS, Lee SH, Jeong BS, Chang HW, Jahng Y, Lee ES, Son JK: Lignans from the roots of Saururus chinensis. J Nat Prod. 2008 Oct;71(10):1771-4. doi: 10.1021/np8002723. Epub 2008 Oct 8. [PubMed:18841903 ]
LOTUS database [Link]

Showing NP-Card for 6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol (NP0218406)

MOL for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

3D MOL for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

3D SDF for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

3D-SDF for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

PDB for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

3D PDB for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

SMILES for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

INCHI for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

Structure for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)

3D Structure for NP0218406 (6-[(2r,3r,4s)-4-(2h-1,3-benzodioxol-5-yl)-4-hydroxy-2,3-dimethylbutyl]-2h-1,3-benzodioxol-5-ol)