NP-MRD: Showing NP-Card for 5-O-Methylembelin (NP0051624)

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Record Information

Version

2.0

Created at

2022-04-27 22:55:28 UTC

Updated at

2022-04-27 22:55:28 UTC

NP-MRD ID

NP0051624

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-O-Methylembelin

Description

5-O-Methylembelin belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively. 5-O-Methylembelin is found in Aegiceras corniculatum, Apis cerana, Averrhoa carambola , Embelia ribes, Embelia schimperi, Glycine max, Lysimachia punctata, Myrsine africana and Trypanosoma brucei. 5-O-Methylembelin was first documented in 2000 (PMID: 11054840). 5-O-Methylembelin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 50 50  0  0  0  0  0  0  0  0999 V2000
   -4.5415   -1.5195   -0.6274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7460   -0.1698   -1.1808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8976    0.9009   -0.5912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0187    1.1952    0.8455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6279    0.1953    1.8491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1740   -0.1975    1.8496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2626    0.9691    2.1312 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1738    0.5184    2.1315 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6547   -0.0731    0.8546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5414    0.9107   -0.2926 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0300    0.3025   -1.5805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4274   -0.1215   -1.5413 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7199   -1.3942   -1.7512 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6821   -2.2851   -2.0027 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1064   -1.8791   -1.7241 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3950   -3.0713   -1.9196 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1833   -0.9317   -1.4590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9327    0.3502   -1.2438 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9747    1.2607   -0.9884 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2299    1.5580    0.3875 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5422    0.7820   -1.2811 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2967    1.9880   -1.0794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3416   -1.7687    0.1136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5760   -1.7197   -0.1551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6107   -2.3028   -1.4524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8464    0.0941   -1.1255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5059   -0.2001   -2.2984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1914    1.8560   -1.1475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8369    0.6449   -0.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1324    1.3902    1.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5914    2.2234    1.0969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8191    0.6895    2.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2479   -0.6888    1.8603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8564   -0.6151    0.8858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0015   -0.9661    2.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4558    1.4368    3.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3804    1.7230    1.3387 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8635    1.3756    2.3762 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3496   -0.2546    2.9376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7270   -0.3649    0.9777 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0979   -0.9826    0.6049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387    1.1288   -0.4216 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0269    1.8756   -0.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8488    1.0508   -2.3789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3756   -0.5559   -1.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8339   -3.2474   -1.7193 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2259   -1.2541   -1.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3570    1.9953    0.8831 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4760    0.6046    0.9270 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1284    2.2045    0.4656 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
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 18 21  1  0
 21 22  2  0
 21 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  2 27  1  0
  3 28  1  0
  3 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  7 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
  9 41  1  0
 10 42  1  0
 10 43  1  0
 11 44  1  0
 11 45  1  0
 14 46  1  0
 17 47  1  0
 20 48  1  0
 20 49  1  0
 20 50  1  0
M  END


  Mrv0541 05061312122D          

 22 22  0  0  0  0            999 V2000
    6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  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
 12 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 13  2  0  0  0  0
 17 14  2  0  0  0  0
 17 15  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 19 15  2  0  0  0  0
 20 17  1  0  0  0  0
 21 18  2  0  0  0  0
 22  2  1  0  0  0  0
 22 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051624

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O4/c1-3-4-5-6-7-8-9-10-11-12-14-17(20)15(19)13-16(22-2)18(14)21/h13,20H,3-12H2,1-2H3

> <INCHI_KEY>
KHBJLRRAMCJZLZ-UHFFFAOYSA-N

> <FORMULA>
C18H28O4

> <MOLECULAR_WEIGHT>
308.4125

> <EXACT_MASS>
308.198759384

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
36.545068315513454

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
4.47

> <JCHEM_LOGP>
4.940862977333335

> <ALOGPS_LOGS>
-5.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.190878539724274

> <JCHEM_PKA_STRONGEST_BASIC>
-4.145569726815219

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
90.08189999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.91e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-O-methylembelin

> <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      12.003   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      32.008   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.337   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.671   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.004   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.672   3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.005   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.339   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      22.673   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.006   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      25.340   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.341   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      26.674   3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      28.007   5.390   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.341   3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.674   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      28.007   2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.007   6.930   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.340   5.390   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      28.007   0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      30.675   2.310   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   22                                                            
CONECT    3    1    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   12                                                       
CONECT   12   11   14                                                       
CONECT   13   15   16                                                       
CONECT   14   12   17   18                                                  
CONECT   15   13   17   19                                                  
CONECT   16   13   18   22                                                  
CONECT   17   14   15   20                                                  
CONECT   18   14   16   21                                                  
CONECT   19   15                                                            
CONECT   20   17                                                            
CONECT   21   18                                                            
CONECT   22    2   16                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Value	Source
2-Hydroxy-5-methoxy-3-undecyl-1,4-benzoquinone	ChEBI
5-O-Methylembelin	MeSH

Chemical Formula

C₁₈H₂₈O₄

Average Mass

308.4125 Da

Monoisotopic Mass

308.19876 Da

IUPAC Name

2-hydroxy-5-methoxy-3-undecylcyclohexa-2,5-diene-1,4-dione

Traditional Name

5-O-methylembelin

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCCC1=C(O)C(=O)C=C(OC)C1=O

InChI Identifier

InChI=1S/C18H28O4/c1-3-4-5-6-7-8-9-10-11-12-14-17(20)15(19)13-16(22-2)18(14)21/h13,20H,3-12H2,1-2H3

InChI Key

KHBJLRRAMCJZLZ-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, 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
Aegiceras corniculatum	Plant	KNApSAcK
Apis cerana	LOTUS Database	35616633
Averrhoa carambola	Plant	KNApSAcK
Embelia ribes	LOTUS Database	35616633
Embelia schimperi	LOTUS Database	35616633
Glycine max	LOTUS Database	35616633
Lysimachia punctata	LOTUS Database	35616633
Myrsine africana	Plant	KNApSAcK
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as p-benzoquinones. These are benzoquinones where the two C=O groups are attached at the 1- and 4-positions, respectively.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

P-benzoquinones

Alternative Parents

Substituents

P-benzoquinone
Vinylogous ester
Vinylogous acid
Enol
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

hydroxybenzoquinone (CHEBI:65842 )
enol ether (CHEBI:65842 )

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	4.47	ALOGPS
logP	4.94	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	8.19	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	90.08 m³·mol⁻¹	ChemAxon
Polarizability	36.55 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

HMDB0040867

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

171489

PDB ID

Not Available

ChEBI ID

65842

Good Scents ID

Not Available

References

General References

Hussein G, Miyashiro H, Nakamura N, Hattori M, Kakiuchi N, Shimotohno K: Inhibitory effects of sudanese medicinal plant extracts on hepatitis C virus (HCV) protease. Phytother Res. 2000 Nov;14(7):510-6. doi: 10.1002/1099-1573(200011)14:7<510::aid-ptr646>3.0.co;2-b. [PubMed:11054840 ]

Showing NP-Card for 5-O-Methylembelin (NP0051624)

MOL for NP0051624 (5-O-Methylembelin)

3D MOL for NP0051624 (5-O-Methylembelin)

3D SDF for NP0051624 (5-O-Methylembelin)

3D-SDF for NP0051624 (5-O-Methylembelin)

PDB for NP0051624 (5-O-Methylembelin)

3D PDB for NP0051624 (5-O-Methylembelin)

SMILES for NP0051624 (5-O-Methylembelin)

INCHI for NP0051624 (5-O-Methylembelin)

Structure for NP0051624 (5-O-Methylembelin)

3D Structure for NP0051624 (5-O-Methylembelin)