NP-MRD: Showing NP-Card for dodoviscin D (NP0036649)

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Record Information

Version

2.0

Created at

2021-06-20 19:46:00 UTC

Updated at

2021-06-30 00:08:24 UTC

NP-MRD ID

NP0036649

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dodoviscin D

Provided By

JEOL Database JEOL Logo

Description

Dodoviscin D belongs to the class of organic compounds known as 3'-prenylated flavones. These are flavones that features a C5-isoprenoid substituent at the 3'-position. dodoviscin D is found in Dodonaea viscosa. dodoviscin D was first documented in 2012 (Zhang, L. -B., et al.). Based on a literature review very few articles have been published on dodoviscin D.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202121463D          

 68 70  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306202121463D          

 68 70  0  0  0  0            999 V2000
    1.7259   -7.5484   -3.3892 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0036649

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C(OC([H])([H])[H])C(O[H])=C2C(=O)C(OC([H])([H])[H])=C(OC2=C1[H])C1=C([H])C(=C(O[H])C(=C1[H])C([H])([H])[C@]([H])(O[H])C(O[H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C27H32O9/c1-13(2)7-8-14-9-16(10-15(21(14)30)11-19(29)27(3,4)33)24-26(35-6)23(32)20-18(36-24)12-17(28)25(34-5)22(20)31/h7,9-10,12,19,28-31,33H,8,11H2,1-6H3/t19-/m0/s1

> <INCHI_KEY>
RYRNVVMPKVKDKR-IBGZPJMESA-N

> <FORMULA>
C27H32O9

> <MOLECULAR_WEIGHT>
500.544

> <EXACT_MASS>
500.20463261

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.05632476676756

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{3-[(2S)-2,3-dihydroxy-3-methylbutyl]-4-hydroxy-5-(3-methylbut-2-en-1-yl)phenyl}-5,7-dihydroxy-3,6-dimethoxy-4H-chromen-4-one

> <ALOGPS_LOGP>
3.60

> <JCHEM_LOGP>
3.731716097333333

> <ALOGPS_LOGS>
-4.84

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.199625788147593

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.900402697375807

> <JCHEM_PKA_STRONGEST_BASIC>
-3.094053189648559

> <JCHEM_POLAR_SURFACE_AREA>
145.91

> <JCHEM_REFRACTIVITY>
136.92889999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.25e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{3-[(2S)-2,3-dihydroxy-3-methylbutyl]-4-hydroxy-5-(3-methylbut-2-en-1-yl)phenyl}-5,7-dihydroxy-3,6-dimethoxychromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 70  0  0  0  0  0  0  0  0999 V2000
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  1 38  1  0
  1 39  1  0
 36 68  1  0
 31 65  1  0
 31 66  1  0
 31 67  1  0
 11 42  1  0
 28 64  1  0
 19 52  1  0
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 23 56  1  0
 25 57  1  0
 25 58  1  0
 25 59  1  0
 26 60  1  0
 26 61  1  0
 26 62  1  0
 27 63  1  0
M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0       1.726  -7.548  -3.389  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.687  -6.291  -4.051  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.140  -5.222  -3.387  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.145  -4.044  -4.152  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.663  -4.053  -5.421  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.640  -2.843  -3.672  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.108  -2.801  -2.389  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.373  -1.592  -1.965  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.926  -1.501  -0.701  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.402  -0.140  -0.385  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.738   0.096  -0.041  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.195   1.390   0.260  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.639   1.583   0.665  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.872   1.220   2.109  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.552   0.171   2.612  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.684  -0.009   4.102  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.220  -0.903   1.799  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.283   2.453   0.215  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.743   3.698   0.550  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.945   2.253  -0.162  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.050   3.392  -0.280  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.479   3.942   1.089  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.583   4.784   1.591  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.792   4.771   1.076  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.024   3.910   0.787  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.735   5.957   0.110  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.933   5.332   2.398  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.519   0.946  -0.457  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.027  -2.521   0.174  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.536  -2.331   1.450  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.514  -3.293   1.835  0.00  0.00           C+0
HETATM   32  C   UNK     0      -0.489  -3.845  -0.249  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.502  -4.838   0.475  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.086  -3.950  -1.602  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.603  -5.168  -2.094  0.00  0.00           C+0
HETATM   36  O   UNK     0       0.585  -6.297  -1.313  0.00  0.00           O+0
HETATM   37  H   UNK     0       2.181  -8.267  -4.078  0.00  0.00           H+0
HETATM   38  H   UNK     0       2.361  -7.510  -2.499  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.718  -7.912  -3.165  0.00  0.00           H+0
HETATM   40  H   UNK     0       1.958  -4.974  -5.569  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.661  -1.955  -4.296  0.00  0.00           H+0
HETATM   42  H   UNK     0      -3.439  -0.734   0.006  0.00  0.00           H+0
HETATM   43  H   UNK     0      -5.275   1.010  -0.016  0.00  0.00           H+0
HETATM   44  H   UNK     0      -4.949   2.624   0.514  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.424   1.931   2.804  0.00  0.00           H+0
HETATM   46  H   UNK     0      -6.741  -0.012   4.391  0.00  0.00           H+0
HETATM   47  H   UNK     0      -5.236  -0.959   4.410  0.00  0.00           H+0
HETATM   48  H   UNK     0      -5.189   0.790   4.664  0.00  0.00           H+0
HETATM   49  H   UNK     0      -6.064  -0.798   0.724  0.00  0.00           H+0
HETATM   50  H   UNK     0      -5.832  -1.886   2.085  0.00  0.00           H+0
HETATM   51  H   UNK     0      -7.300  -0.893   1.980  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.994   4.220   0.915  0.00  0.00           H+0
HETATM   53  H   UNK     0      -0.408   4.180  -0.891  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.921   3.034  -0.840  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.583   3.127   1.817  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.154   5.355   2.266  0.00  0.00           H+0
HETATM   57  H   UNK     0       3.943   4.485   0.947  0.00  0.00           H+0
HETATM   58  H   UNK     0       3.072   3.056   1.473  0.00  0.00           H+0
HETATM   59  H   UNK     0       3.034   3.531  -0.238  0.00  0.00           H+0
HETATM   60  H   UNK     0       2.633   6.578   0.208  0.00  0.00           H+0
HETATM   61  H   UNK     0       1.659   5.633  -0.932  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.886   6.613   0.334  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.218   4.621   3.000  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.515   0.768  -0.747  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.141  -2.838   2.608  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.036  -4.173   2.273  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.163  -3.576   0.999  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.195  -6.074  -0.437  0.00  0.00           H+0
CONECT    1    2   37   38   39                                             
CONECT    2    3    1                                                       
CONECT    3    2    4   35                                                  
CONECT    4    6    3    5                                                  
CONECT    5    4   40                                                       
CONECT    6    7    4   41                                                  
CONECT    7    6   34    8                                                  
CONECT    8    9    7                                                       
CONECT    9   10   29    8                                                  
CONECT   10    9   11   28                                                  
CONECT   11   10   12   42                                                  
CONECT   12   13   11   18                                                  
CONECT   13   14   12   43   44                                             
CONECT   14   13   15   45                                                  
CONECT   15   16   17   14                                                  
CONECT   16   15   46   47   48                                             
CONECT   17   15   49   50   51                                             
CONECT   18   12   20   19                                                  
CONECT   19   18   52                                                       
CONECT   20   18   28   21                                                  
CONECT   21   20   22   53   54                                             
CONECT   22   21   24   23   55                                             
CONECT   23   22   56                                                       
CONECT   24   22   25   26   27                                             
CONECT   25   24   57   58   59                                             
CONECT   26   24   60   61   62                                             
CONECT   27   24   63                                                       
CONECT   28   20   10   64                                                  
CONECT   29   30   32    9                                                  
CONECT   30   29   31                                                       
CONECT   31   30   65   66   67                                             
CONECT   32   33   34   29                                                  
CONECT   33   32                                                            
CONECT   34    7   32   35                                                  
CONECT   35   36    3   34                                                  
CONECT   36   35   68                                                       
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    5                                                            
CONECT   41    6                                                            
CONECT   42   11                                                            
CONECT   43   13                                                            
CONECT   44   13                                                            
CONECT   45   14                                                            
CONECT   46   16                                                            
CONECT   47   16                                                            
CONECT   48   16                                                            
CONECT   49   17                                                            
CONECT   50   17                                                            
CONECT   51   17                                                            
CONECT   52   19                                                            
CONECT   53   21                                                            
CONECT   54   21                                                            
CONECT   55   22                                                            
CONECT   56   23                                                            
CONECT   57   25                                                            
CONECT   58   25                                                            
CONECT   59   25                                                            
CONECT   60   26                                                            
CONECT   61   26                                                            
CONECT   62   26                                                            
CONECT   63   27                                                            
CONECT   64   28                                                            
CONECT   65   31                                                            
CONECT   66   31                                                            
CONECT   67   31                                                            
CONECT   68   36                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  140    0
END

RDKit          3D

68 70  0  0  0  0  0  0  0  0999 V2000
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 27 63  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₂O₉

Average Mass

500.5440 Da

Monoisotopic Mass

500.20463 Da

IUPAC Name

2-{3-[(2S)-2,3-dihydroxy-3-methylbutyl]-4-hydroxy-5-(3-methylbut-2-en-1-yl)phenyl}-5,7-dihydroxy-3,6-dimethoxy-4H-chromen-4-one

Traditional Name

2-{3-[(2S)-2,3-dihydroxy-3-methylbutyl]-4-hydroxy-5-(3-methylbut-2-en-1-yl)phenyl}-5,7-dihydroxy-3,6-dimethoxychromen-4-one

CAS Registry Number

Not Available

SMILES

[H]OC1=C(OC([H])([H])[H])C(O[H])=C2C(=O)C(OC([H])([H])[H])=C(OC2=C1[H])C1=C([H])C(=C(O[H])C(=C1[H])C([H])([H])[C@]([H])(O[H])C(O[H])(C([H])([H])[H])C([H])([H])[H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]

InChI Identifier

InChI=1S/C27H32O9/c1-13(2)7-8-14-9-16(10-15(21(14)30)11-19(29)27(3,4)33)24-26(35-6)23(32)20-18(36-24)12-17(28)25(34-5)22(20)31/h7,9-10,12,19,28-31,33H,8,11H2,1-6H3/t19-/m0/s1

InChI Key

RYRNVVMPKVKDKR-IBGZPJMESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, acetone-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Dodonaea viscosa	JEOL database	Zhang, L. -B., et al, J. Nat. Prod. 75, 699 (2012)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3'-prenylated flavones. These are flavones that features a C5-isoprenoid substituent at the 3'-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavones

Direct Parent

3'-prenylated flavones

Alternative Parents

Substituents

3'-prenylated flavone
3-methoxyflavonoid-skeleton
6-methoxyflavonoid-skeleton
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
3-methoxychromone
Chromone
Benzopyran
1-benzopyran
Anisole
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Pyranone
Benzenoid
Pyran
Monocyclic benzene moiety
Tertiary alcohol
Vinylogous acid
Heteroaromatic compound
Secondary alcohol
1,2-diol
Ether
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Alcohol
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	3.6	ALOGPS
logP	3.73	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	6.9	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	145.91 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	136.93 m³·mol⁻¹	ChemAxon
Polarizability	54.06 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	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

27445005

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57409965

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang, L. -B., et al. (2012). Zhang, L. -B., et al, J. Nat. Prod. 75, 699 (2012). J. Nat. Prod..

Showing NP-Card for dodoviscin D (NP0036649)

MOL for NP0036649 (dodoviscin D)

3D MOL for NP0036649 (dodoviscin D)

3D SDF for NP0036649 (dodoviscin D)

3D-SDF for NP0036649 (dodoviscin D)

PDB for NP0036649 (dodoviscin D)

3D PDB for NP0036649 (dodoviscin D)

SMILES for NP0036649 (dodoviscin D)

INCHI for NP0036649 (dodoviscin D)

Structure for NP0036649 (dodoviscin D)

3D Structure for NP0036649 (dodoviscin D)