NP-MRD: Showing NP-Card for Sequirin A (NP0072408)

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Record Information

Version

2.0

Created at

2022-04-28 17:45:33 UTC

Updated at

2022-04-28 17:45:33 UTC

NP-MRD ID

NP0072408

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Sequirin A

Description

Sugiresinol, also known as sequirin a, belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed. Sequirin A is found in Cryptomeria japonica and Sequoia sempervirens. Sequirin A was first documented in 2003 (PMID: 15369328). Based on a literature review a small amount of articles have been published on sugiresinol (PMID: 17191998).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    5.8868    2.3018    0.6056 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7205    1.5919    0.4161 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0962    0.8750    1.4155 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9284    0.1778    1.1806 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3423    0.1763   -0.0758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1164   -0.5276   -0.4137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0986    0.0451    0.3409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2953   -0.6600   -0.2492 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5866   -0.0683    0.0601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7150    1.1507    0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9830    1.6902    0.9525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1155    0.9925    0.6129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3988    1.5077    0.8819 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9939   -0.2308   -0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7422   -0.7423   -0.2674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1976   -2.0039    0.1078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1724   -2.5709   -0.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1872   -2.0221   -0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0993   -2.5100   -1.1737 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9925    0.9022   -1.0492 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1529    1.6029   -0.8419 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3145    2.2974    1.5407 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5534    0.8721    2.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4436   -0.3818    1.9663 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8757   -0.3592   -1.4822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1015    1.1427    0.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0065   -0.2305    1.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1252   -0.6303   -1.3639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8549    1.7099    0.9461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0751    2.6560    1.4368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8209    1.2764    1.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8671   -0.7974   -0.2767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6681   -1.7100   -0.7525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1710   -3.6772   -0.4746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3325   -2.3917   -1.6896 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5247   -2.3388    0.7573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8846   -2.2195   -2.0894 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5858    0.9466   -2.0695 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6169    2.1573   -1.6549 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18 17  1  0
 17 16  1  0
 16  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 21  1  0
 21 20  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
  6 18  1  0
 20  5  1  0
 15  9  1  0
 19 37  1  0
 18 36  1  1
 17 34  1  0
 17 35  1  0
  8 28  1  6
  7 26  1  0
  7 27  1  0
  6 25  1  6
  4 24  1  0
  3 23  1  0
  1 22  1  0
 21 39  1  0
 20 38  1  0
 10 29  1  0
 11 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
M  END


  Mrv1652304282219452D          

 21 23  0  0  1  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  6  0  0  0
  3  8  1  1  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
 11 14  1  0  0  0  0
  1 15  1  1  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
 18 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072408

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C17H18O4/c18-13-5-1-11(2-6-13)15-9-17(21-10-16(15)20)12-3-7-14(19)8-4-12/h1-8,15-20H,9-10H2/t15-,16+,17+/m0/s1

> <INCHI_KEY>
JQRWWSPNQHLXDY-GVDBMIGSSA-N

> <FORMULA>
C17H18O4

> <MOLECULAR_WEIGHT>
286.327

> <EXACT_MASS>
286.12050906

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.80231193046518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,4S,6R)-4,6-bis(4-hydroxyphenyl)oxan-3-ol

> <ALOGPS_LOGP>
2.07

> <JCHEM_LOGP>
2.5758983026666664

> <ALOGPS_LOGS>
-3.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.206476107697187

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.383885121508646

> <JCHEM_PKA_STRONGEST_BASIC>
-3.201783923059855

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
79.3272

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.03e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sugiresinol

> <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       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    6   15                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4                                                            
CONECT    8    3    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11                                                            
CONECT   15    1   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21   18                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
(-)-Sugiresinol	ChEBI
(3S)-Tetrahydro-4alpha,6alpha-bis(4-hydroxyphenyl)-2H-pyran-3-ol	ChEBI
Sequirin a	ChEBI
Sequirin-a	ChEBI
(3S)-Tetrahydro-4a,6a-bis(4-hydroxyphenyl)-2H-pyran-3-ol	Generator
(3S)-Tetrahydro-4α,6α-bis(4-hydroxyphenyl)-2H-pyran-3-ol	Generator

Chemical Formula

C₁₇H₁₈O₄

Average Mass

286.3270 Da

Monoisotopic Mass

286.12051 Da

IUPAC Name

(3S,4S,6R)-4,6-bis(4-hydroxyphenyl)oxan-3-ol

Traditional Name

sugiresinol

CAS Registry Number

Not Available

SMILES

O[C@@H]1CO[C@H](C[C@H]1C1=CC=C(O)C=C1)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C17H18O4/c18-13-5-1-11(2-6-13)15-9-17(21-10-16(15)20)12-3-7-14(19)8-4-12/h1-8,15-20H,9-10H2/t15-,16+,17+/m0/s1

InChI Key

JQRWWSPNQHLXDY-GVDBMIGSSA-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
Cryptomeria japonica	Plant	KNApSAcK
Sequoia sempervirens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Not Available

Sub Class

Not Available

Direct Parent

Lignans, neolignans and related compounds

Alternative Parents

Substituents

Norlignan skeleton
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Oxane
Benzenoid
Secondary alcohol
Dialkyl ether
Ether
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

norlignan (CHEBI:53645 )

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	2.07	ALOGPS
logP	2.58	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	9.38	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.92 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	79.33 m³·mol⁻¹	ChemAxon
Polarizability	28.8 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00032262

Chemspider ID

20045089

KEGG Compound ID

C20133

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12443127

PDB ID

Not Available

ChEBI ID

53645

Good Scents ID

Not Available

References

General References

Zhang YM, Tan NH, Yang YB, Lu Y, Cao P, Wu YS: Norlignans from Sequoia sempervirens. Chem Biodivers. 2005 Apr;2(4):497-505. doi: 10.1002/cbdv.200590030. [PubMed:17191998 ]
Evans PA, Leahy DK: Regioselective and enantiospecific rhodium-catalyzed allylic alkylation reactions using copper(I) enolates: synthesis of (-)-sugiresinol dimethyl ether. J Am Chem Soc. 2003 Jul 30;125(30):8974-5. doi: 10.1021/ja035983p. [PubMed:15369328 ]

Showing NP-Card for Sequirin A (NP0072408)

MOL for NP0072408 (Sequirin A)

3D MOL for NP0072408 (Sequirin A)

3D SDF for NP0072408 (Sequirin A)

3D-SDF for NP0072408 (Sequirin A)

PDB for NP0072408 (Sequirin A)

3D PDB for NP0072408 (Sequirin A)

SMILES for NP0072408 (Sequirin A)

INCHI for NP0072408 (Sequirin A)

Structure for NP0072408 (Sequirin A)

3D Structure for NP0072408 (Sequirin A)