NP-MRD: Showing NP-Card for Daphnodorin D1 (NP0056062)

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Record Information

Version

2.0

Created at

2022-04-28 01:56:52 UTC

Updated at

2022-04-28 01:56:53 UTC

NP-MRD ID

NP0056062

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daphnodorin D1

Description

Daphnodorin D2 belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''. Daphnodorin D1 is found in Daphne odora and Wikstroemia sikokiana. Daphnodorin D1 was first documented in 2011 (PMID: 21837973). Based on a literature review very few articles have been published on daphnodorin D2.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282203562D          

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M  END

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  Mrv1652304282203562D          

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 34 37  1  0  0  0  0
  3 38  1  0  0  0  0
  1 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056062

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=C(C=C1)[C@@H]1CCC2=C(O)C=C(O)C(=C2O1)C1=C(OC2=CC(O)=CC(O)=C2C1=O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H22O9/c31-16-5-1-14(2-6-16)23-10-9-19-20(34)13-22(36)26(30(19)38-23)27-28(37)25-21(35)11-18(33)12-24(25)39-29(27)15-3-7-17(32)8-4-15/h1-8,11-13,23,31-36H,9-10H2/t23-/m0/s1

> <INCHI_KEY>
KBUYUAWZPKKJRC-QHCPKHFHSA-N

> <FORMULA>
C30H22O9

> <MOLECULAR_WEIGHT>
526.497

> <EXACT_MASS>
526.126382288

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
52.32661837128866

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-8-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
4.32

> <JCHEM_LOGP>
5.575107057

> <ALOGPS_LOGS>
-4.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.946986322298415

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.507137914398905

> <JCHEM_PKA_STRONGEST_BASIC>
-4.803911291824559

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
141.96530000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.85e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-8-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one

> <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      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.335  -4.620   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  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.001   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  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -4.906  -1.064   0.000  0.00  0.00           O+0
CONECT    1    2    6   39                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   38                                                  
CONECT    4    3    5   30                                                  
CONECT    5    4    6   27                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   24                                                  
CONECT   11   10   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18   14                                                       
CONECT   20   17                                                            
CONECT   21   11   22                                                       
CONECT   22   21   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   10   25                                                  
CONECT   25   24                                                            
CONECT   26   22                                                            
CONECT   27    5   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29    4                                                       
CONECT   31   28   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38    3                                                            
CONECT   39    1                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₂O₉

Average Mass

526.4970 Da

Monoisotopic Mass

526.12638 Da

IUPAC Name

3-[(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-8-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one

Traditional Name

3-[(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-8-yl]-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one

CAS Registry Number

Not Available

SMILES

OC1=CC=C(C=C1)[C@@H]1CCC2=C(O)C=C(O)C(=C2O1)C1=C(OC2=CC(O)=CC(O)=C2C1=O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C30H22O9/c31-16-5-1-14(2-6-16)23-10-9-19-20(34)13-22(36)26(30(19)38-23)27-28(37)25-21(35)11-18(33)12-24(25)39-29(27)15-3-7-17(32)8-4-15/h1-8,11-13,23,31-36H,9-10H2/t23-/m0/s1

InChI Key

KBUYUAWZPKKJRC-QHCPKHFHSA-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
Daphne odora	Plant	KNApSAcK
Wikstroemia sikokiana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biflavonoids and polyflavonoids. These are organic compounds containing at least two flavan/flavone units. These units are usually linked through CC or C-O-C bonds. Some examples include C2-O-C3, C2-O-C4, C3'-C3''', and C6-C8''.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Biflavonoids and polyflavonoids

Direct Parent

Biflavonoids and polyflavonoids

Alternative Parents

Substituents

Bi- and polyflavonoid skeleton
Pyranoisoflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Hydroxyisoflavonoid
7-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Isoflavone
Flavan
Isoflavonoid skeleton
Isoflavonoid
Chromone
Benzopyran
1-benzopyran
Chromane
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Benzenoid
Monocyclic benzene moiety
Pyran
Vinylogous acid
Heteroaromatic compound
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Organic oxide
Organooxygen compound
Hydrocarbon derivative
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	4.32	ALOGPS
logP	5.58	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	6.51	ChemAxon
pKa (Strongest Basic)	-4.8	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	141.97 m³·mol⁻¹	ChemAxon
Polarizability	52.33 Å³	ChemAxon
Number of Rings	6	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

Not Available

Chemspider ID

26358120

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13941113

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Peng J, Yu Y, Xiong W, Wan C, Cao S: [Chemical constituents of Daphne odora var. margirmta]. Zhongguo Zhong Yao Za Zhi. 2011 May;36(10):1316-8. [PubMed:21837973 ]

Showing NP-Card for Daphnodorin D1 (NP0056062)

MOL for NP0056062 (Daphnodorin D1)

3D MOL for NP0056062 (Daphnodorin D1)

3D SDF for NP0056062 (Daphnodorin D1)

3D-SDF for NP0056062 (Daphnodorin D1)

PDB for NP0056062 (Daphnodorin D1)

3D PDB for NP0056062 (Daphnodorin D1)

SMILES for NP0056062 (Daphnodorin D1)

INCHI for NP0056062 (Daphnodorin D1)

Structure for NP0056062 (Daphnodorin D1)

3D Structure for NP0056062 (Daphnodorin D1)