NP-MRD: Showing NP-Card for Daphnodorin B (NP0056187)

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Record Information

Version

2.0

Created at

2022-04-28 02:02:17 UTC

Updated at

2022-04-28 02:02:17 UTC

NP-MRD ID

NP0056187

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Daphnodorin B

Description

Daphnodorin B belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety. Daphnodorin B is found in Daphne feddei, Daphne genkwa, Daphne odora , Daphne papyracea, Stellera chamaejasme, Stellera chamaejasme L. , Wikstroemia indica and Wikstroemia sikokiana. Daphnodorin B was first documented in 2011 (PMID: 21837973). Based on a literature review a small amount of articles have been published on Daphnodorin B (PMID: 31315443) (PMID: 25096753) (PMID: 25076123) (PMID: 24007373).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282204022D          

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M  END

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M  END


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  3 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
 30 32  1  1  0  0  0
 29 33  1  6  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
 36 39  1  0  0  0  0
  1 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056187

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O)C=C3OC(=C(C(=O)C4=C(O)C=C(O)C=C4O)C3=C2O[C@@H]1C1=CC=C(O)C=C1)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H22O10/c31-15-5-1-13(2-6-15)28-22(37)11-18-19(34)12-23-25(30(18)40-28)26(29(39-23)14-3-7-16(32)8-4-14)27(38)24-20(35)9-17(33)10-21(24)36/h1-10,12,22,28,31-37H,11H2/t22-,28+/m0/s1

> <INCHI_KEY>
JBNFGJOTOPTIDE-RBISFHTESA-N

> <FORMULA>
C30H22O10

> <MOLECULAR_WEIGHT>
542.496

> <EXACT_MASS>
542.121296908

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
53.45068081096416

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(11S,12R)-8,11-dihydroxy-4,12-bis(4-hydroxyphenyl)-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,3,6,8-tetraene-3-carbonyl]benzene-1,3,5-triol

> <ALOGPS_LOGP>
3.69

> <JCHEM_LOGP>
5.673679295666666

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.949370562324404

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.88590257313019

> <JCHEM_PKA_STRONGEST_BASIC>
-2.918962985147242

> <JCHEM_POLAR_SURFACE_AREA>
181.04999999999998

> <JCHEM_REFRACTIVITY>
142.39180000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(11S,12R)-8,11-dihydroxy-4,12-bis(4-hydroxyphenyl)-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,3,6,8-tetraene-3-carbonyl]benzene-1,3,5-triol

> <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       0.369  -4.158   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.180  -2.849   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.452  -1.492   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.087  -1.444   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.898  -2.753   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.170  -4.110   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.394  -2.386   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.507  -0.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.081  -0.268   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.641   1.256   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.620   2.420   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.826   2.294   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.305   1.864   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.416   2.929   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.049   4.425   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.571   4.855   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.459   3.789   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.199   4.777   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -6.161   5.491   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -3.763   0.322   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -4.816  -0.039   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.173  -0.767   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -7.482   0.045   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -7.434   1.584   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.077   2.312   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.768   1.501   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -9.028   2.108   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.263  -0.183   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.803  -0.231   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.531  -1.588   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.719  -2.897   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.050  -2.225   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.614   1.078   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.886   2.435   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.697   3.744   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.237   3.696   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.965   2.339   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.153   1.030   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       6.142   5.076   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       1.020  -5.682   0.000  0.00  0.00           O+0
CONECT    1    2    6   40                                                  
CONECT    2    1    3   31                                                  
CONECT    3    2    4   28                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   21                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   17                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   12   18                                                  
CONECT   18   17                                                            
CONECT   19   15                                                            
CONECT   20   13                                                            
CONECT   21    8   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   21                                                       
CONECT   27   24                                                            
CONECT   28    3   29                                                       
CONECT   29   28   30   33                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30    2                                                       
CONECT   32   30                                                            
CONECT   33   29   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   39                                                  
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
CONECT   39   36                                                            
CONECT   40    1                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₂O₁₀

Average Mass

542.4960 Da

Monoisotopic Mass

542.12130 Da

IUPAC Name

2-[(11S,12R)-8,11-dihydroxy-4,12-bis(4-hydroxyphenyl)-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,3,6,8-tetraene-3-carbonyl]benzene-1,3,5-triol

Traditional Name

2-[(11S,12R)-8,11-dihydroxy-4,12-bis(4-hydroxyphenyl)-5,13-dioxatricyclo[7.4.0.0^{2,6}]trideca-1,3,6,8-tetraene-3-carbonyl]benzene-1,3,5-triol

CAS Registry Number

Not Available

SMILES

O[C@H]1CC2=C(O)C=C3OC(=C(C(=O)C4=C(O)C=C(O)C=C4O)C3=C2O[C@@H]1C1=CC=C(O)C=C1)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C30H22O10/c31-15-5-1-13(2-6-15)28-22(37)11-18-19(34)12-23-25(30(18)40-28)26(29(39-23)14-3-7-16(32)8-4-14)27(38)24-20(35)9-17(33)10-21(24)36/h1-10,12,22,28,31-37H,11H2/t22-,28+/m0/s1

InChI Key

JBNFGJOTOPTIDE-RBISFHTESA-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 feddei	LOTUS Database	35616633
Daphne genkwa	LOTUS Database	35616633
Daphne odora	Plant	KNApSAcK
Daphne papyracea	LOTUS Database	35616633
Stellera chamaejasme	LOTUS Database	35616633
Stellera chamaejasme L.	Plant	KNApSAcK
Wikstroemia indica	LOTUS Database	35616633
Wikstroemia sikokiana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

2-arylbenzofuran flavonoids

Sub Class

Not Available

Direct Parent

2-arylbenzofuran flavonoids

Alternative Parents

Substituents

2-arylbenzofuran flavonoid
Furanoflavonoid or dihydroflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Hydroxyflavonoid
Flavan-3-ol
Flavan
2-phenylbenzofuran
Phenylbenzofuran
Aryl-phenylketone
Chromane
1-benzopyran
Benzopyran
Phloroglucinol derivative
Benzenetriol
Benzofuran
Benzoyl
Aryl ketone
3-aroylfuran
Phenol
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Vinylogous acid
Heteroaromatic compound
Furan
Ketone
Secondary alcohol
Ether
Polyol
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
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	3.69	ALOGPS
logP	5.67	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	6.89	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	181.05 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	142.39 m³·mol⁻¹	ChemAxon
Polarizability	53.45 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

C00008955

Chemspider ID

65355

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72427

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Badawy A, Hassanean H, Ibrahim AK, Habib ES, El-Magd MA, Ahmed SA: Isolates From Thymelaea Hirsuta Inhibit Progression Of Hepatocellular Carcinoma In Vitro And In Vivo. Nat Prod Res. 2021 Jun;35(11):1799-1807. doi: 10.1080/14786419.2019.1643859. Epub 2019 Jul 17. [PubMed:31315443 ]
Yan Z, Guo H, Yang J, Liu Q, Jin H, Xu R, Cui H, Qin B: Phytotoxic flavonoids from roots of Stellera chamaejasme L. (Thymelaeaceae). Phytochemistry. 2014 Oct;106:61-68. doi: 10.1016/j.phytochem.2014.07.013. Epub 2014 Aug 2. [PubMed:25096753 ]
Ghanem H, Haba H, Marcourt L, Benkhaled M, Wolfender JL: Microphynolides A and B, new spiro-gamma-lactone glycosides from Thymelaea microphylla. Nat Prod Res. 2014;28(20):1732-8. doi: 10.1080/14786419.2014.942662. Epub 2014 Jul 30. [PubMed:25076123 ]
Yuan H, Bi KJ, Li B, Yue RC, Ye J, Shen YH, Shan L, Jin HZ, Sun QY, Zhang WD: Construction of 2-substituted-3-functionalized benzofurans via intramolecular Heck coupling: application to enantioselective total synthesis of daphnodorin B. Org Lett. 2013 Sep 20;15(18):4742-5. doi: 10.1021/ol4021095. Epub 2013 Sep 5. [PubMed:24007373 ]
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 B (NP0056187)

MOL for NP0056187 (Daphnodorin B)

3D MOL for NP0056187 (Daphnodorin B)

3D SDF for NP0056187 (Daphnodorin B)

3D-SDF for NP0056187 (Daphnodorin B)

PDB for NP0056187 (Daphnodorin B)

3D PDB for NP0056187 (Daphnodorin B)

SMILES for NP0056187 (Daphnodorin B)

INCHI for NP0056187 (Daphnodorin B)

Structure for NP0056187 (Daphnodorin B)

3D Structure for NP0056187 (Daphnodorin B)