NP-MRD: Showing NP-Card for (2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one (NP0259863)

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Record Information

Version

2.0

Created at

2022-09-08 01:52:09 UTC

Updated at

2022-09-08 01:52:09 UTC

NP-MRD ID

NP0259863

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one

Description

Gericudranin D belongs to the class of organic compounds known as curcuminoids. These are aromatic compounds containing a curcumin moiety, which is composed of two aryl buten-2-one (feruloyl) chromophores joined by a methylene group. (2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one is found in Maclura tricuspidata. Based on a literature review very few articles have been published on gericudranin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082203522D          

 37 41  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 O   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
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    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   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
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309082203522D          

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M  END
> <DATABASE_ID>
NP0259863

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@H](OC2=C(CC3=CC=C(O)C=C3)C(O)=C(CC3=CC=C(O)C=C3)C(O)=C2C1=O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H24O8/c30-18-7-1-15(2-8-18)13-21-24(33)22(14-16-3-9-19(31)10-4-16)29-23(25(21)34)26(35)27(36)28(37-29)17-5-11-20(32)12-6-17/h1-12,27-28,30-34,36H,13-14H2/t27-,28+/m0/s1

> <INCHI_KEY>
LHFMOLHENFWCMZ-WUFINQPMSA-N

> <FORMULA>
C29H24O8

> <MOLECULAR_WEIGHT>
500.503

> <EXACT_MASS>
500.147117733

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
49.4282435255609

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one

> <JCHEM_LOGP>
5.696407000333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.103723482665249

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.277387638407943

> <JCHEM_PKA_STRONGEST_BASIC>
-4.034566016631119

> <JCHEM_POLAR_SURFACE_AREA>
147.68

> <JCHEM_REFRACTIVITY>
136.06420000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4   26                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8                                                       
CONECT   15    6   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   26                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   19                                                       
CONECT   26   17    3   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   36                                                  
CONECT   29   28   30   35                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   29                                                       
CONECT   36   28    2   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₂₄O₈

Average Mass

500.5030 Da

Monoisotopic Mass

500.14712 Da

IUPAC Name

(2R,3R)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(2R,3R)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@H](OC2=C(CC3=CC=C(O)C=C3)C(O)=C(CC3=CC=C(O)C=C3)C(O)=C2C1=O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C29H24O8/c30-18-7-1-15(2-8-18)13-21-24(33)22(14-16-3-9-19(31)10-4-16)29-23(25(21)34)26(35)27(36)28(37-29)17-5-11-20(32)12-6-17/h1-12,27-28,30-34,36H,13-14H2/t27-,28+/m0/s1

InChI Key

LHFMOLHENFWCMZ-WUFINQPMSA-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
Maclura tricuspidata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as curcuminoids. These are aromatic compounds containing a curcumin moiety, which is composed of two aryl buten-2-one (feruloyl) chromophores joined by a methylene group.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Diarylheptanoids

Sub Class

Linear diarylheptanoids

Direct Parent

Curcuminoids

Alternative Parents

Substituents

Bis-desmethoxycurcumin
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavanone
Flavanonol
Hydroxyflavonoid
Flavan
Chromone
Chromane
Benzopyran
1-benzopyran
Aryl alkyl ketone
Aryl ketone
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Vinylogous acid
Secondary alcohol
Ketone
Polyol
Ether
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organic oxide
Alcohol
Hydrocarbon derivative
Organooxygen compound
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	5.7	ChemAxon
pKa (Strongest Acidic)	6.28	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	147.68 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	136.06 m³·mol⁻¹	ChemAxon
Polarizability	49.43 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00008658

Chemspider ID

23327523

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44559901

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one (NP0259863)

MOL for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

3D MOL for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

3D SDF for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

3D-SDF for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

PDB for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

3D PDB for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

SMILES for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

INCHI for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

Structure for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)

3D Structure for NP0259863 ((2r,3r)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)-6,8-bis[(4-hydroxyphenyl)methyl]-2,3-dihydro-1-benzopyran-4-one)