NP-MRD: Showing NP-Card for 2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione (NP0274481)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-08 21:53:23 UTC

Updated at

2022-09-08 21:53:23 UTC

NP-MRD ID

NP0274481

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione

Description

Myrsinone 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). 2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione is found in Myrsine africana and Myrsine melanophloeos. Myrsinone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 47 47  0  0  0  0  0  0  0  0999 V2000
   -5.5397   -2.4416    0.9034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4138   -1.0439    0.3221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -1.1689   -1.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8384    0.1384   -1.8136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8001    1.0327   -1.1932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4303    0.3984   -1.1862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4825    1.3856   -0.5434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0609    0.8470   -0.4826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8198    1.8634    0.1589 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2367    1.3752    0.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3726    0.1074    1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8105   -0.2738    1.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4582   -0.3471    2.2213 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8648   -0.7145    2.3165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4715   -0.7818    3.4239 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6363   -1.0228    1.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9761   -1.3715    1.2200 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0191   -0.9578   -0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7487   -1.2505   -1.1883 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5944   -0.5851   -0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0487   -0.5373   -1.2655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5752   -2.8490    1.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2642   -2.3994    1.7295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9713   -3.1200    0.1308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7330   -0.4244    0.9293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4201   -0.5823    0.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0837   -1.7848   -1.1835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7944   -1.7371   -1.6407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8131    0.6442   -1.9456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4794   -0.0905   -2.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7239    1.9395   -1.8392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0287    1.3586   -0.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0721    0.2366   -2.2382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4293   -0.5741   -0.6517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8365    1.5260    0.5019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5254    2.3268   -1.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0135   -0.0919    0.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2453    0.6246   -1.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8222    2.8361   -0.4060 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5096    2.0734    1.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6587    1.2179   -0.8043 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9139    2.1575    0.6742 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0404    0.2800    2.0610 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8127   -0.7309    0.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8818   -0.1189    3.0989 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7050   -1.0363    0.6360 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6842   -0.5744   -1.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 20 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 13 45  1  0
 17 46  1  0
 19 47  1  0
M  END


  Mrv0541 05061312002D          

 21 21  0  0  0  0            999 V2000
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  2  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 17 16  2  0  0  0  0
 18 14  2  0  0  0  0
 19 15  2  0  0  0  0
 20 16  1  0  0  0  0
 21 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0274481

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCCC1=CC(=O)C(O)=C(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H26O4/c1-2-3-4-5-6-7-8-9-10-11-13-12-14(18)16(20)17(21)15(13)19/h12,20-21H,2-11H2,1H3

> <INCHI_KEY>
JPFXYNDBKFIYLX-UHFFFAOYSA-N

> <FORMULA>
C17H26O4

> <MOLECULAR_WEIGHT>
294.3859

> <EXACT_MASS>
294.18310932

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
34.57723501510914

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione

> <ALOGPS_LOGP>
4.28

> <JCHEM_LOGP>
4.8280355880000005

> <ALOGPS_LOGS>
-4.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.31285030428159

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.009260551963592

> <JCHEM_PKA_STRONGEST_BASIC>
-4.086790698805616

> <JCHEM_POLAR_SURFACE_AREA>
74.60000000000001

> <JCHEM_REFRACTIVITY>
85.33069999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.85e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.003 -11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.337 -12.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.671 -11.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.004 -12.320   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.338 -11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.005 -11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      18.672 -12.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.339 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      18.672 -13.860   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.339 -13.860   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.005 -14.630   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      22.673 -11.550   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      17.338 -14.630   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      22.673 -14.630   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      20.005 -16.170   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   13                                                       
CONECT   12   13   14                                                       
CONECT   13   11   12   15                                                  
CONECT   14   12   16   18                                                  
CONECT   15   13   17   19                                                  
CONECT   16   14   17   20                                                  
CONECT   17   15   16   21                                                  
CONECT   18   14                                                            
CONECT   19   15                                                            
CONECT   20   16                                                            
CONECT   21   17                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Value	Source
2,3-Dihydroxy-5-undecyl-2,5-cyclohexadiene-1,4-dione, 9ci	HMDB

Chemical Formula

C₁₇H₂₆O₄

Average Mass

294.3859 Da

Monoisotopic Mass

294.18311 Da

IUPAC Name

2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione

Traditional Name

2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCCC1=CC(=O)C(O)=C(O)C1=O

InChI Identifier

InChI=1S/C17H26O4/c1-2-3-4-5-6-7-8-9-10-11-13-12-14(18)16(20)17(21)15(13)19/h12,20-21H,2-11H2,1H3

InChI Key

JPFXYNDBKFIYLX-UHFFFAOYSA-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
Myrsine africana	LOTUS Database	35616633
Myrsine melanophloeos	LOTUS Database	35616633

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
Quinone
P-benzoquinone
Vinylogous acid
Cyclic ketone
Ketone
Enediol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	4.28	ALOGPS
logP	4.83	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	8.01	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	85.33 m³·mol⁻¹	ChemAxon
Polarizability	34.58 Å³	ChemAxon
Number of Rings	1	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

HMDB0040646

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020439

KNApSAcK ID

Not Available

Chemspider ID

30777500

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

137177207

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione (NP0274481)

MOL for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

3D MOL for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

3D SDF for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

3D-SDF for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

PDB for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

3D PDB for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

SMILES for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

INCHI for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

Structure for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)

3D Structure for NP0274481 (2,3-dihydroxy-5-undecylcyclohexa-2,5-diene-1,4-dione)