NP-MRD: Showing NP-Card for 2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol (NP0284410)

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Record Information

Version

2.0

Created at

2022-09-09 12:05:55 UTC

Updated at

2022-09-09 12:05:55 UTC

NP-MRD ID

NP0284410

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol

Description

AC1L7357 belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones. 2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol is found in Hypoxis nyasica and Hypoxis obtusa. AC1L7357 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 04121514292D          

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M  END

     RDKit          3D

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M  END


  Mrv0541 04121514292D          

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   -4.2868  -17.3250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013  -17.7375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868  -16.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013  -16.0875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579  -14.0250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434  -13.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145  -11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -9.9000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -9.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -7.4250    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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 11 10  1  4  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 21 30  1  0  0  0  0
 30 31  1  0  0  0  0
 19 32  1  0  0  0  0
 32 33  2  0  0  0  0
 16 33  1  0  0  0  0
 10 34  1  0  0  0  0
 34 35  2  0  0  0  0
  7 35  1  0  0  0  0
  5 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 38 40  1  0  0  0  0
  3 40  1  0  0  0  0
 40 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0284410

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC=C(C=CC(C=C)C3=CC=C(OC4OC(CO)C(O)C(O)C4O)C=C3)C=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C29H36O12/c1-2-16(17-7-11-19(12-8-17)39-29-27(37)25(35)23(33)21(14-31)41-29)6-3-15-4-9-18(10-5-15)38-28-26(36)24(34)22(32)20(13-30)40-28/h2-12,16,20-37H,1,13-14H2

> <INCHI_KEY>
AROSPRRPXMWTNY-UHFFFAOYSA-N

> <FORMULA>
C29H36O12

> <MOLECULAR_WEIGHT>
576.595

> <EXACT_MASS>
576.220676599

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
59.56216960359836

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.28

> <JCHEM_LOGP>
-0.040711538666665145

> <ALOGPS_LOGS>
-3.22

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.421312841026612

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.899111777757593

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343686494

> <JCHEM_POLAR_SURFACE_AREA>
198.76

> <JCHEM_REFRACTIVITY>
143.55810000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         0                                  
HETATM    1  O   UNK     0      -4.001 -11.550   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334 -14.630   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334 -16.170   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000 -16.940   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000 -18.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334 -19.250   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334 -20.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000 -21.560   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000 -23.100   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334 -23.870   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334 -25.410   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000 -26.180   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.000 -27.720   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667 -26.180   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.667 -27.720   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001 -28.490   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.335 -27.720   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -6.668 -28.490   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -6.668 -30.030   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -5.335 -30.800   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.335 -32.340   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.001 -33.110   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.667 -32.340   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -6.668 -33.110   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -6.668 -34.650   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -8.002 -32.340   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -9.336 -33.110   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -8.002 -30.800   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -9.336 -30.030   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.335 -26.180   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.001 -25.410   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.334 -20.790   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334 -19.250   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -2.667 -18.480   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -5.335 -16.940   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -5.335 -13.860   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   40                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   36                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   35                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   34                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   33                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   32                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   30                                                  
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   30                                                  
CONECT   29   28                                                            
CONECT   30   28   21   31                                                  
CONECT   31   30                                                            
CONECT   32   19   33                                                       
CONECT   33   32   16                                                       
CONECT   34   10   35                                                       
CONECT   35   34    7                                                       
CONECT   36    5   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38    3   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₆O₁₂

Average Mass

576.5950 Da

Monoisotopic Mass

576.22068 Da

IUPAC Name

2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol

Traditional Name

2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC=C(C=CC(C=C)C3=CC=C(OC4OC(CO)C(O)C(O)C4O)C=C3)C=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C29H36O12/c1-2-16(17-7-11-19(12-8-17)39-29-27(37)25(35)23(33)21(14-31)41-29)6-3-15-4-9-18(10-5-15)38-28-26(36)24(34)22(32)20(13-30)40-28/h2-12,16,20-37H,1,13-14H2

InChI Key

AROSPRRPXMWTNY-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Hypoxis nyasica	LOTUS Database	35616633
Hypoxis obtusa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
Fatty acyl glycoside
Phenolic glycoside
Fatty acyl glycoside of mono- or disaccharide
Linear 1,3-diarylpropanoid
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Phenoxy compound
Phenol ether
Styrene
Oxane
Monosaccharide
Fatty acyl
Monocyclic benzene moiety
Benzenoid
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Primary alcohol
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
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	0.28	ALOGPS
logP	-0.041	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	11.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	198.76 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	143.56 m³·mol⁻¹	ChemAxon
Polarizability	59.56 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

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

353841

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol (NP0284410)

MOL for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

3D MOL for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

3D SDF for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

3D-SDF for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

PDB for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

3D PDB for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

SMILES for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

INCHI for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

Structure for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)

3D Structure for NP0284410 (2-(hydroxymethyl)-6-{4-[3-(4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)penta-1,4-dien-1-yl]phenoxy}oxane-3,4,5-triol)