NP-MRD: Showing NP-Card for Compound 4 (NP0332274)

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Record Information

Version

2.0

Created at

2023-12-21 12:02:34 UTC

Updated at

2024-09-03 04:18:40 UTC

NP-MRD ID

NP0332274

Natural Product DOI

https://doi.org/10.57994/1469

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Compound 4

Description

Compound 4 belongs to the class of organic compounds known as 7,9'-epoxylignans. These are lignans that contain the 7,9'-epoxylignan skeleton, which consists of a tetrahydrofuran that carries a phenyl group, a methyl group, and a benzyl group at the 2-, 3-, 4-position, respectively. Compound 4 was first documented in 2024 (PMID: 39311441). Based on a literature review a small amount of articles have been published on Compound 4 (PMID: 39309099) (PMID: 39297735) (PMID: 39301842).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 12212312022D          

 30 32  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0206   -0.8630    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -2.3058    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0032   -5.3493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -5.4355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  2  0  0  0  0
  3 12  1  0  0  0  0
 13  2  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  6  0  0  0
 13 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 17 20  1  1  0  0  0
 17 21  1  0  0  0  0
 21 15  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 24 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 22 30  1  0  0  0  0
M  END


  Mrv2104 12212312022D          

 30 32  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0206   -0.8630    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -2.3058    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0032   -5.3493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8237   -5.4355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034   -3.0882    0.0000 C   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  9 12  2  0  0  0  0
  3 12  1  0  0  0  0
 13  2  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 16  1  6  0  0  0
 13 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 17 20  1  1  0  0  0
 17 21  1  0  0  0  0
 21 15  1  0  0  0  0
 21 22  1  1  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 24 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 22 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332274

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CO[C@@H](C2=CC(OC)=C(O)C=C2)[C@]1([H])CO)[C@H](O)C1=CC=C(OC)C(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C21H26O7/c1-25-17-7-5-12(8-19(17)27-3)20(24)15-11-28-21(14(15)10-22)13-4-6-16(23)18(9-13)26-2/h4-9,14-15,20-24H,10-11H2,1-3H3/t14-,15+,20-,21+/m1/s1

> <INCHI_KEY>
VXNZZNFSNWJGNR-CALQCPNCSA-N

> <FORMULA>
C21H26O7

> <MOLECULAR_WEIGHT>
390.432

> <EXACT_MASS>
390.167853177

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
41.008086924251415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-[(2R,3S,4R)-4-[(S)-(3,4-dimethoxyphenyl)(hydroxy)methyl]-3-(hydroxymethyl)oxolan-2-yl]-2-methoxyphenol

> <JCHEM_LOGP>
1.2619500310000002

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.069389776694074

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.910716771831664

> <JCHEM_PKA_STRONGEST_BASIC>
-2.641369821635834

> <JCHEM_POLAR_SURFACE_AREA>
97.61000000000001

> <JCHEM_REFRACTIVITY>
103.09259999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2R,3S,4R)-4-[(S)-(3,4-dimethoxyphenyl)(hydroxy)methyl]-3-(hydroxymethyl)oxolan-2-yl]-2-methoxyphenol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-DEC-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-DEC-23         0                                  
HETATM    1  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.104  -4.680   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      -0.038  -1.611   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.377  -2.739   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.521  -3.770   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0      -1.001  -4.304   0.000  0.00  0.00           H+0
HETATM   21  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.342  -5.926   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.285  -7.333   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.620  -8.578   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.006  -9.985   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.538 -10.146   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.152  -8.417   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.057  -9.663   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.778  -7.011   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.873  -5.765   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9    3                                                       
CONECT   13    2   14   16   17                                             
CONECT   14   13   15                                                       
CONECT   15   14   21                                                       
CONECT   16   13                                                            
CONECT   17   13   18   20   21                                             
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17                                                            
CONECT   21   17   15   22                                                  
CONECT   22   21   23   30                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   22                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₆O₇

Average Mass

390.4320 Da

Monoisotopic Mass

390.16785 Da

IUPAC Name

4-[(2R,3S,4R)-4-[(S)-(3,4-dimethoxyphenyl)(hydroxy)methyl]-3-(hydroxymethyl)oxolan-2-yl]-2-methoxyphenol

Traditional Name

4-[(2R,3S,4R)-4-[(S)-(3,4-dimethoxyphenyl)(hydroxy)methyl]-3-(hydroxymethyl)oxolan-2-yl]-2-methoxyphenol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CO[C@@H](C2=CC(OC)=C(O)C=C2)[C@]1([H])CO)[C@H](O)C1=CC=C(OC)C(OC)=C1

InChI Identifier

InChI=1S/C21H26O7/c1-25-17-7-5-12(8-19(17)27-3)20(24)15-11-28-21(14(15)10-22)13-4-6-16(23)18(9-13)26-2/h4-9,14-15,20-24H,10-11H2,1-3H3/t14-,15+,20-,21+/m1/s1

InChI Key

VXNZZNFSNWJGNR-CALQCPNCSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	Not Available	Keio University	Haruhisa Kikuchi	2024-03-06	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	Not Available	Keio University	Haruhisa Kikuchi	2024-03-06	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	Not Available	Keio University	Haruhisa Kikuchi	2024-03-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)	Not Available	Keio University	Haruhisa Kikuchi	2024-03-06	View Spectrum
HMQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	Not Available	Keio University	Haruhisa Kikuchi	2024-03-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	halkiku@keio.jp	Keio University	Haruhisa Kikuchi	2024-05-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)	halkiku@keio.jp	Keio University	Haruhisa Kikuchi	2024-05-14	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
pseudopereskiifolia		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as 7,9'-epoxylignans. These are lignans that contain the 7,9'-epoxylignan skeleton, which consists of a tetrahydrofuran that carries a phenyl group, a methyl group, and a benzyl group at the 2-, 3-, 4-position, respectively.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Furanoid lignans

Sub Class

Tetrahydrofuran lignans

Direct Parent

7,9'-epoxylignans

Alternative Parents

Substituents

7,9p-epoxylignan
Methoxyphenol
Fatty alcohol
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Fatty acyl
Benzenoid
Monocyclic benzene moiety
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Aromatic alcohol
Organooxygen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.26	ChemAxon
pKa (Strongest Acidic)	9.91	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	97.61 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	103.09 m³·mol⁻¹	ChemAxon
Polarizability	41.01 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	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhu T, Li C, Tang J, Chen L, Yu G, Yang Y, Cheng G, Xiao C, Yang H: High-Energy and Thermally Stable Energetic Materials Based on an Azo-Fused Dinitramino Compound. Org Lett. 2024 Sep 23. doi: 10.1021/acs.orglett.4c03345. [PubMed:39311441 ]
Wan Z, Wang Y, Lu H, Wei R, Yin H, Zeng H, Azam M, Luo J, Jia C: Incorporation of 2D pyreneammonium iodide for enhancing the efficiency and stability of perovskite solar cells. Chem Sci. 2024 Sep 11. doi: 10.1039/d4sc04819a. [PubMed:39309099 ]
Hamed A, El Gaafary M, Fumiko Yamaguchi L, Stammler HG, Salih LM, Ziegler D, Syrovets T, Kato MJ: Chemical constituents of Coccoloba peltata Schott leaves and their cytotoxic activities. Nat Prod Res. 2024 Sep 19:1-7. doi: 10.1080/14786419.2024.2405011. [PubMed:39297735 ]
Chen JX, Yang XQ, Sun J, Li YH, Yang YB, Ding ZT: New Antifungal and Antifeedant Metabolites from Daldinia eschscholtzii Cocultured with Colletotrichum pseudomajus. Chem Biodivers. 2024 Sep 20:e202401726. doi: 10.1002/cbdv.202401726. [PubMed:39301842 ]

Showing NP-Card for Compound 4 (NP0332274)

MOL for NP0332274 (Compound 4)

3D MOL for NP0332274 (Compound 4)

3D SDF for NP0332274 (Compound 4)

3D-SDF for NP0332274 (Compound 4)

PDB for NP0332274 (Compound 4)

3D PDB for NP0332274 (Compound 4)

SMILES for NP0332274 (Compound 4)

INCHI for NP0332274 (Compound 4)

Structure for NP0332274 (Compound 4)

3D Structure for NP0332274 (Compound 4)