NP-MRD: Showing NP-Card for (2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid (NP0306402)

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Record Information

Version

2.0

Created at

2022-09-10 22:50:51 UTC

Updated at

2022-09-10 22:50:51 UTC

NP-MRD ID

NP0306402

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid

Description

Herbarin A belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. (2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid is found in Aplysina aerophoba. (2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid was first documented in 2015 (PMID: 25690788). Based on a literature review very few articles have been published on Herbarin A.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 29  0  0  0  0  0  0  0  0999 V2000
   -5.1921    0.5406   -0.4503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0387   -0.1516   -0.0709 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7587    0.3174   -0.3147 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6203    1.5269   -0.9636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3528    2.0149   -1.2177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2031    3.1261   -1.8137 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3367    1.3120   -0.8335 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4059    0.1533   -0.2114 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8389   -0.5117    0.1539 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0275   -0.0072   -0.1095 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2681   -0.6751    0.2573 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4462   -0.1441   -0.0203 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7065   -0.7597    0.3185 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7713   -1.8592    0.9096 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8875   -0.1291   -0.0127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6361   -0.3856    0.0702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7247   -1.6711    0.7603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2547    1.5257    0.0479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2440    0.7421   -1.5421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0706   -0.0707   -0.1617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4676    2.1267   -1.2913 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8262   -1.4694    0.6683 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0958    0.9413   -0.6186 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2650   -1.6396    0.7755 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4311    0.8069   -0.5314 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8917    0.3798   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9770   -1.6597    1.6032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7052   -1.8459    1.2544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4677   -2.5338    0.1246 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  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
  8 16  2  0
 16 17  1  0
 16  3  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  4 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 15 26  1  0
 17 27  1  0
 17 28  1  0
 17 29  1  0
M  END


  Mrv1652309112200502D          

 17 17  0  0  0  0            999 V2000
    1.4289    2.4750    0.0000 C   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
    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
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   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
   -0.7145   -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
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    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
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 O   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    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 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
  8 16  2  0  0  0  0
  3 16  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0306402

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=O)OC(\C=C\C=C\C(O)=O)=C1C

> <INCHI_IDENTIFIER>
InChI=1S/C12H12O5/c1-8-9(5-3-4-6-11(13)14)17-12(15)7-10(8)16-2/h3-7H,1-2H3,(H,13,14)/b5-3+,6-4+

> <INCHI_KEY>
ISQQPILYSRJHBC-GGWOSOGESA-N

> <FORMULA>
C12H12O5

> <MOLECULAR_WEIGHT>
236.223

> <EXACT_MASS>
236.068473486

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.62745665024734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E)-5-(4-methoxy-5-methyl-2-oxo-2H-pyran-6-yl)penta-2,4-dienoic acid

> <JCHEM_LOGP>
1.2330662286666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.165306575475273

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8345767138113125

> <JCHEM_POLAR_SURFACE_AREA>
72.83

> <JCHEM_REFRACTIVITY>
64.88840000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -8.002   0.000   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   16                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    8    3   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₂O₅

Average Mass

236.2230 Da

Monoisotopic Mass

236.06847 Da

IUPAC Name

(2E,4E)-5-(4-methoxy-5-methyl-2-oxo-2H-pyran-6-yl)penta-2,4-dienoic acid

Traditional Name

(2E,4E)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid

CAS Registry Number

Not Available

SMILES

COC1=CC(=O)OC(\C=C\C=C\C(O)=O)=C1C

InChI Identifier

InChI=1S/C12H12O5/c1-8-9(5-3-4-6-11(13)14)17-12(15)7-10(8)16-2/h3-7H,1-2H3,(H,13,14)/b5-3+,6-4+

InChI Key

ISQQPILYSRJHBC-GGWOSOGESA-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
Aplysina aerophoba	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Alkyl aryl ether
Heterocyclic fatty acid
Pyranone
Pyran
Unsaturated fatty acid
Heteroaromatic compound
Vinylogous ester
Lactone
Carboxylic acid derivative
Carboxylic acid
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.23	ChemAxon
pKa (Strongest Acidic)	4.17	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	64.89 m³·mol⁻¹	ChemAxon
Polarizability	23.63 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9217883

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11042715

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Heimberger J, Cade HC, Padgett J, Sittaramane V, Shaikh A: Total synthesis of Herbarin A and B, determination of their antioxidant properties and toxicity in zebrafish embryo model. Bioorg Med Chem Lett. 2015 Mar 15;25(6):1192-5. doi: 10.1016/j.bmcl.2015.01.065. Epub 2015 Feb 4. [PubMed:25690788 ]
LOTUS database [Link]

Showing NP-Card for (2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid (NP0306402)

MOL for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

3D MOL for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

3D SDF for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

3D-SDF for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

PDB for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

3D PDB for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

SMILES for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

INCHI for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

Structure for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)

3D Structure for NP0306402 ((2e,4e)-5-(4-methoxy-3-methyl-6-oxopyran-2-yl)penta-2,4-dienoic acid)