NP-MRD: Showing NP-Card for Isobiflorin (NP0049685)

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Record Information

Version

2.0

Created at

2022-03-17 21:16:27 UTC

Updated at

2022-03-17 21:16:27 UTC

NP-MRD ID

NP0049685

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Isobiflorin

Description

Isobiflorin, also known as clove 3, belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. Isobiflorin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Isobiflorin has been detected, but not quantified in, cloves and herbs and spices. Isobiflorin is found in Aloe vera, Baeckea frutescens, Dryopteris crassirhizoma and Eucalyptus cypellocarpa. This could make isobiflorin a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061312002D          

 25 27  0  0  0  0            999 V2000
    0.7145   -0.4125    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
    4.2868    0.8250    0.0000 C   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
    1.4289    0.0000    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
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    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
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    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   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  2  0  0  0  0
 12  9  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 10  2  0  0  0  0
 15 11  1  0  0  0  0
 16 11  1  0  0  0  0
 16 14  1  0  0  0  0
 17  4  1  0  0  0  0
 18  6  2  0  0  0  0
 19  7  1  0  0  0  0
 20  8  1  0  0  0  0
 21 12  1  0  0  0  0
 22 13  1  0  0  0  0
 23 14  1  0  0  0  0
 24  5  1  0  0  0  0
 24 15  1  0  0  0  0
 25  9  1  0  0  0  0
 25 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049685

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=CC(=O)C2=C(O1)C(C1OC(CO)C(O)C(O)C1O)=C(O)C=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C16H18O9/c1-5-2-6(18)10-7(19)3-8(20)11(15(10)24-5)16-14(23)13(22)12(21)9(4-17)25-16/h2-3,9,12-14,16-17,19-23H,4H2,1H3

> <INCHI_KEY>
UDTUCCXZNVRBEJ-UHFFFAOYSA-N

> <FORMULA>
C16H18O9

> <MOLECULAR_WEIGHT>
354.3087

> <EXACT_MASS>
354.095082174

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
33.50469918908068

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-2-methyl-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

> <ALOGPS_LOGP>
-0.67

> <JCHEM_LOGP>
-0.8428982790000001

> <ALOGPS_LOGS>
-1.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.281189075104272

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.2169068694819165

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979192629260984

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
84.18730000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-methyl-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002   0.000   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       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    5    6                                                       
CONECT    3    7    8                                                       
CONECT    4    9   17                                                       
CONECT    5    1    2   24                                                  
CONECT    6    2   10   18                                                  
CONECT    7    3   10   19                                                  
CONECT    8    3   11   20                                                  
CONECT    9    4   12   25                                                  
CONECT   10    6    7   15                                                  
CONECT   11    8   15   16                                                  
CONECT   12    9   13   21                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   16   23                                                  
CONECT   15   10   11   24                                                  
CONECT   16   11   14   25                                                  
CONECT   17    4                                                            
CONECT   18    6                                                            
CONECT   19    7                                                            
CONECT   20    8                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
CONECT   24    5   15                                                       
CONECT   25    9   16                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Value	Source
8-b-D-Glucopyranosyl-5,7-dihydroxy-2-methyl-4H-1-benzopyran-4-one	HMDB
8-C-Glucopyranosylnoreugenin	HMDB
8-Glucosyl-5,7-dihydroxy-2-methylchromone	HMDB
Clove 3	HMDB

Chemical Formula

C₁₆H₁₈O₉

Average Mass

354.3087 Da

Monoisotopic Mass

354.09508 Da

IUPAC Name

5,7-dihydroxy-2-methyl-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-2-methyl-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one

CAS Registry Number

152041-16-2

SMILES

CC1=CC(=O)C2=C(O1)C(C1OC(CO)C(O)C(O)C1O)=C(O)C=C2O

InChI Identifier

InChI=1S/C16H18O9/c1-5-2-6(18)10-7(19)3-8(20)11(15(10)24-5)16-14(23)13(22)12(21)9(4-17)25-16/h2-3,9,12-14,16-17,19-23H,4H2,1H3

InChI Key

UDTUCCXZNVRBEJ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Aloe vera	LOTUS Database	35616633
Baeckea frutescens	LOTUS Database	35616633
Dryopteris crassirhizoma	Plant	KNApSAcK
Eucalyptus cypellocarpa	LOTUS Database	35616633
Syzygium aromaticum	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Hexose monosaccharide
C-glycosyl compound
Chromone
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Monosaccharide
Oxane
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Oxacycle
Dialkyl ether
Ether
Organoheterocyclic compound
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
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	-0.67	ALOGPS
logP	-0.84	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	6.22	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.91 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	84.19 m³·mol⁻¹	ChemAxon
Polarizability	33.5 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0040632

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020423

KNApSAcK ID

C00030518

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

85114699

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Isobiflorin (NP0049685)

MOL for NP0049685 (Isobiflorin)

3D MOL for NP0049685 (Isobiflorin)

3D SDF for NP0049685 (Isobiflorin)

3D-SDF for NP0049685 (Isobiflorin)

PDB for NP0049685 (Isobiflorin)

3D PDB for NP0049685 (Isobiflorin)

SMILES for NP0049685 (Isobiflorin)

INCHI for NP0049685 (Isobiflorin)

Structure for NP0049685 (Isobiflorin)

3D Structure for NP0049685 (Isobiflorin)