NP-MRD: Showing NP-Card for Methylpedicinin (NP0054863)

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Record Information

Version

2.0

Created at

2022-04-28 01:04:52 UTC

Updated at

2022-04-28 01:04:52 UTC

NP-MRD ID

NP0054863

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Methylpedicinin

Description

Methylpedicinin belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6). Thus, methylpedicinin is considered to be a flavonoid. Methylpedicinin is found in Didymocarpus pedicellata . Based on a literature review very few articles have been published on Methylpedicinin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    6.0417    0.3329   -0.4067 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8742    0.3029   -1.1974 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6056    0.5506   -0.7166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6419   -0.2541   -1.0732 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8778   -1.3387   -1.9176 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1274   -2.6309   -1.3780 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2534   -0.0191   -0.5732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3916   -0.8148   -0.9474 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9122    1.0764    0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3688    1.4091    0.8497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3191    2.5045    1.6342 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6896    0.9263    0.8119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3219   -0.0524    0.2504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7526   -0.3640    0.3631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5789    0.4079    1.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9373    0.1320    1.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4553   -0.9387    0.5862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6351   -1.7267   -0.1810 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2953   -1.4477   -0.2959 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    1.8620    0.6252 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7453    2.9502    1.4690 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3180    1.6451    0.1473 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2429    2.4269    0.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0401   -0.3830    0.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2710    1.3501   -0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8854    0.0531   -1.0748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0293   -2.6341   -0.7265 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2862   -3.3313   -2.2217 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2577   -2.9717   -0.7820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4189    1.5525    1.4401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7734   -0.7200   -0.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2530    1.2752    1.6732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5431    0.7768    1.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5295   -1.1339    0.6991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0867   -2.5786   -0.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6528   -2.0618   -0.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8427    3.8667    1.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 22  3  1  0
 19 14  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  6 27  1  0
  6 28  1  0
  6 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 16 33  1  0
 17 34  1  0
 18 35  1  0
 19 36  1  0
 21 37  1  0
M  END


  Mrv1652304282203042D          

 23 24  0  0  0  0            999 V2000
    2.1434   -2.8875    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
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    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
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   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
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   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
    6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 11 17  1  0  0  0  0
 17 18  2  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  1  0  0  0  0
 12 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054863

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(OC)C(=O)C(C(=O)\C=C\C2=CC=CC=C2)=C(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H14O6/c1-22-16-14(20)12(13(19)15(21)17(16)23-2)11(18)9-8-10-6-4-3-5-7-10/h3-9,19H,1-2H3/b9-8+

> <INCHI_KEY>
HRKCLRLMUHTQGG-CMDGGOBGSA-N

> <FORMULA>
C17H14O6

> <MOLECULAR_WEIGHT>
314.293

> <EXACT_MASS>
314.079038171

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
31.299453789881014

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-hydroxy-5,6-dimethoxy-3-[(2E)-3-phenylprop-2-enoyl]cyclohexa-2,5-diene-1,4-dione

> <ALOGPS_LOGP>
2.03

> <JCHEM_LOGP>
1.9700961313333334

> <ALOGPS_LOGS>
-4.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8589152597984255

> <JCHEM_PKA_STRONGEST_BASIC>
-4.729270561366278

> <JCHEM_POLAR_SURFACE_AREA>
89.9

> <JCHEM_REFRACTIVITY>
86.47500000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.12e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylpedicinin

> <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  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   17                                                  
CONECT   12   11   13   23                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   21                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   11   18                                                  
CONECT   18   17                                                            
CONECT   19   16   20                                                       
CONECT   20   19                                                            
CONECT   21   15   22                                                       
CONECT   22   21                                                            
CONECT   23   12                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₄O₆

Average Mass

314.2930 Da

Monoisotopic Mass

314.07904 Da

IUPAC Name

2-hydroxy-5,6-dimethoxy-3-[(2E)-3-phenylprop-2-enoyl]cyclohexa-2,5-diene-1,4-dione

Traditional Name

methylpedicinin

CAS Registry Number

Not Available

SMILES

COC1=C(OC)C(=O)C(C(=O)\C=C\C2=CC=CC=C2)=C(O)C1=O

InChI Identifier

InChI=1S/C17H14O6/c1-22-16-14(20)12(13(19)15(21)17(16)23-2)11(18)9-8-10-6-4-3-5-7-10/h3-9,19H,1-2H3/b9-8+

InChI Key

HRKCLRLMUHTQGG-CMDGGOBGSA-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
Didymocarpus pedicellata	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6).

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Ubiquinones

Alternative Parents

Substituents

Ubiquinone skeleton
Cinnamic acid or derivatives
P-benzoquinone
Quinone
Styrene
Monocyclic benzene moiety
Benzenoid
Acryloyl-group
Enone
Vinylogous ester
Vinylogous acid
Alpha,beta-unsaturated ketone
Ketone
Cyclic ketone
Enol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Chalcones and dihydrochalcones (LMPK12120420 )

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	2.03	ALOGPS
logP	1.97	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.86	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	89.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	86.48 m³·mol⁻¹	ChemAxon
Polarizability	31.3 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00007175

Chemspider ID

10296392

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21679829

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Methylpedicinin (NP0054863)

MOL for NP0054863 (Methylpedicinin)

3D MOL for NP0054863 (Methylpedicinin)

3D SDF for NP0054863 (Methylpedicinin)

3D-SDF for NP0054863 (Methylpedicinin)

PDB for NP0054863 (Methylpedicinin)

3D PDB for NP0054863 (Methylpedicinin)

SMILES for NP0054863 (Methylpedicinin)

INCHI for NP0054863 (Methylpedicinin)

Structure for NP0054863 (Methylpedicinin)

3D Structure for NP0054863 (Methylpedicinin)