NP-MRD: Showing NP-Card for Cymopol (NP0079873)

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Record Information

Version

2.0

Created at

2022-04-29 00:57:05 UTC

Updated at

2022-04-29 00:57:05 UTC

NP-MRD ID

NP0079873

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cymopol

Description

Cymopol belongs to the class of organic compounds known as prenylated hydroquinones. These are quinones with a structure characterized by the hydroquinone ring substituted by an prenyl side-chain. Cymopol is found in Cymopolia barbata. Cymopol was first documented in 2003 (PMID: 12762791). Based on a literature review a small amount of articles have been published on Cymopol (PMID: 31536771) (PMID: 14994189).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 40  0  0  0  0  0  0  0  0999 V2000
    5.4419    1.4432    0.8912 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0160    1.0266    0.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0014    2.0037    1.4203 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6968   -0.1779    0.4993 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3034   -0.6572    0.4973 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8195   -1.0322   -0.9067 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4113   -1.4985   -0.7637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1681   -2.6855    0.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6079   -0.9232   -1.3617 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9767   -1.4303   -1.1815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8884   -0.4348   -0.5996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2331   -0.5362    0.7297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0810    0.3536    1.3627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4017    0.2088    2.7165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6213    1.4006    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8048    2.6687    1.4740 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -4.2762    1.5083   -0.6910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4326    0.6169   -1.3057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1099    0.7465   -2.6299 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0440    0.6781    0.3682 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8437    1.6068    1.9069 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5380    2.3896    0.2847 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5131    2.8415    1.9509 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120    1.5501    2.1377 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4047    2.3892    0.5621 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4512   -0.8787    0.1341 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1481   -1.5181    1.1820 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5990    0.1359    0.8631 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7896   -0.1335   -1.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4497   -1.8382   -1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3318   -3.5062   -0.4508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4228   -2.3695    0.9969 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1074   -3.1171    0.4945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4221   -0.0655   -1.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9779   -2.3199   -0.5181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3874   -1.8284   -2.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8425   -1.3412    1.3538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0197    0.8659    3.1603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7244    2.3461   -1.2078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4968    1.5119   -3.1742 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18 11  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  8 31  1  0
  8 32  1  0
  8 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 12 37  1  0
 14 38  1  0
 17 39  1  0
 19 40  1  0
M  END


  Mrv1652304292202572D          

 19 19  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    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
   -2.8579    3.3000    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
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
  4 17  1  0  0  0  0
  2 18  1  0  0  0  0
  1 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0079873

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C\CC1=CC(O)=C(Br)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H21BrO2/c1-11(2)5-4-6-12(3)7-8-13-9-16(19)14(17)10-15(13)18/h5,7,9-10,18-19H,4,6,8H2,1-3H3/b12-7+

> <INCHI_KEY>
IUFDABCKTYWJDR-KPKJPENVSA-N

> <FORMULA>
C16H21BrO2

> <MOLECULAR_WEIGHT>
325.246

> <EXACT_MASS>
324.072493

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
32.361403613473016

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-bromo-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]benzene-1,4-diol

> <ALOGPS_LOGP>
5.11

> <JCHEM_LOGP>
5.523149072333332

> <ALOGPS_LOGS>
-4.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.511604805808133

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.434054747801667

> <JCHEM_PKA_STRONGEST_BASIC>
-6.270551373152155

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
85.688

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-bromo-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]benzene-1,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   18 Br   UNK     0       4.001   2.310   0.000  0.00  0.00          Br+0
HETATM   19  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    6   19                                                  
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   17                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    4                                                            
CONECT   18    2                                                            
CONECT   19    1                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₁BrO₂

Average Mass

325.2460 Da

Monoisotopic Mass

324.07249 Da

IUPAC Name

2-bromo-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]benzene-1,4-diol

Traditional Name

2-bromo-5-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]benzene-1,4-diol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\CC1=CC(O)=C(Br)C=C1O

InChI Identifier

InChI=1S/C16H21BrO2/c1-11(2)5-4-6-12(3)7-8-13-9-16(19)14(17)10-15(13)18/h5,7,9-10,18-19H,4,6,8H2,1-3H3/b12-7+

InChI Key

IUFDABCKTYWJDR-KPKJPENVSA-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
Cymopolia barbata	Viridiplantae	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prenylated hydroquinones. These are quinones with a structure characterized by the hydroquinone ring substituted by an prenyl side-chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Prenylated hydroquinones

Alternative Parents

Substituents

Prenylbenzoquinol
Aromatic monoterpenoid
Monocyclic monoterpenoid
Monoterpenoid
1,4-dihydroxy-2-halobenzenoid
3-halophenol
2-halophenol
Hydroquinone
3-bromophenol
2-bromophenol
1-hydroxy-2-unsubstituted benzenoid
Bromobenzene
Halobenzene
Phenol
Aryl halide
Benzenoid
Monocyclic benzene moiety
Aryl bromide
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organobromide
Organohalogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic 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	5.11	ALOGPS
logP	5.52	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	8.43	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	85.69 m³·mol⁻¹	ChemAxon
Polarizability	32.36 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00044678

Chemspider ID

4533374

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5386672

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bousquet MS, Ratnayake R, Pope JL, Chen QY, Zhu F, Chen S, Carney TJ, Gharaibeh RZ, Jobin C, Paul VJ, Luesch H: Seaweed natural products modify the host inflammatory response via Nrf2 signaling and alter colon microbiota composition and gene expression. Free Radic Biol Med. 2020 Jan;146:306-323. doi: 10.1016/j.freeradbiomed.2019.09.013. Epub 2019 Sep 16. [PubMed:31536771 ]
Takamatsu S, Nagle DG, Gerwick WH: Secondary metabolites from marine cyanobacteria and algae inhibit LFA-1/ICAM-1 mediated cell adhesion. Planta Med. 2004 Feb;70(2):127-31. doi: 10.1055/s-2004-815488. [PubMed:14994189 ]
Takamatsu S, Hodges TW, Rajbhandari I, Gerwick WH, Hamann MT, Nagle DG: Marine natural products as novel antioxidant prototypes. J Nat Prod. 2003 May;66(5):605-8. doi: 10.1021/np0204038. [PubMed:12762791 ]

Showing NP-Card for Cymopol (NP0079873)

MOL for NP0079873 (Cymopol)

3D MOL for NP0079873 (Cymopol)

3D SDF for NP0079873 (Cymopol)

3D-SDF for NP0079873 (Cymopol)

PDB for NP0079873 (Cymopol)

3D PDB for NP0079873 (Cymopol)

SMILES for NP0079873 (Cymopol)

INCHI for NP0079873 (Cymopol)

Structure for NP0079873 (Cymopol)

3D Structure for NP0079873 (Cymopol)