NP-MRD: Showing NP-Card for Nigellic acid (NP0048449)

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Record Information

Version

2.0

Created at

2022-03-17 20:56:39 UTC

Updated at

2022-03-17 20:56:39 UTC

NP-MRD ID

NP0048449

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nigellic acid

Description

Nigellic acid, also known as nigellate, belongs to the class of organic compounds known as abscisic acids and derivatives. These are terpene compounds containing the abscisic acid moiety, which is characterized by a 3-methylpenta-2,4-dienoic acid attached to the C1 carbon of a 4-oxocyclohex-2-ene moiety. Nigellic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Nigellic acid has been detected, but not quantified in, broad beans and pulses. Nigellic acid is found in Nigella damascena and Xanthium strumarium . This could make nigellic acid a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241211582D          

 20 20  0  0  0  0            999 V2000
   -2.4984    0.0007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4984   -0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7842   -1.2378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712   -0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0712    0.0007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7842    0.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1970    1.1277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3714    1.1277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2140   -1.2378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3556   -1.2378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3556    0.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3571    0.0007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0712    0.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7855    0.0007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4997    0.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3556   -0.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0712    1.2378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4997    1.2378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2140    0.0007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3599   -0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  2  9  2  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5 11  1  0  0  0  0
  5 16  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
 10 20  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 17  1  0  0  0  0
 14 15  1  0  0  0  0
 15 18  2  0  0  0  0
 15 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048449

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C1(O)C(CO)=CC(=O)CC1(C)C)=C/C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H20O5/c1-10(6-13(18)19)4-5-15(20)11(9-16)7-12(17)8-14(15,2)3/h4-7,16,20H,8-9H2,1-3H3,(H,18,19)/b5-4+,10-6+

> <INCHI_KEY>
ZGHRCSAIMSBFLK-UMCKCUICSA-N

> <FORMULA>
C15H20O5

> <MOLECULAR_WEIGHT>
280.3163

> <EXACT_MASS>
280.13107375

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
29.199898956385415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E)-5-[1-hydroxy-2-(hydroxymethyl)-6,6-dimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
0.812504336666667

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.323305911740345

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.602616871732804

> <JCHEM_PKA_STRONGEST_BASIC>
-2.78923360219619

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
76.75110000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E)-5-[1-hydroxy-2-(hydroxymethyl)-6,6-dimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -4.664   0.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.664  -1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.331  -2.311   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.000  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.000   0.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.331   0.769   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.101   2.105   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.560   2.105   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.999  -2.311   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.664  -2.311   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.664   0.769   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.667   0.001   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.000   0.769   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.333   0.001   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.666   0.769   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -0.664  -0.769   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.000   2.311   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.666   2.311   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.999   0.001   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.672  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6   11   16                                             
CONECT    6    1    5    7    8                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    2                                                            
CONECT   10    4   20                                                       
CONECT   11    5   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   18   19                                                  
CONECT   16    5                                                            
CONECT   17   13                                                            
CONECT   18   15                                                            
CONECT   19   15                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
Nigellate	Generator
(2E,4E)-5-[1-Hydroxy-2-(hydroxymethyl)-6,6-dimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoate	Generator

Chemical Formula

C₁₅H₂₀O₅

Average Mass

280.3163 Da

Monoisotopic Mass

280.13107 Da

IUPAC Name

(2E,4E)-5-[1-hydroxy-2-(hydroxymethyl)-6,6-dimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

Traditional Name

(2E,4E)-5-[1-hydroxy-2-(hydroxymethyl)-6,6-dimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

CAS Registry Number

91897-25-5

SMILES

C\C(\C=C\C1(O)C(CO)=CC(=O)CC1(C)C)=C/C(O)=O

InChI Identifier

InChI=1S/C15H20O5/c1-10(6-13(18)19)4-5-15(20)11(9-16)7-12(17)8-14(15,2)3/h4-7,16,20H,8-9H2,1-3H3,(H,18,19)/b5-4+,10-6+

InChI Key

ZGHRCSAIMSBFLK-UMCKCUICSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Nigella damascena	Plant	KNApSAcK
Vicia faba	FooDB	KNAPSACK
Xanthium strumarium	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as abscisic acids and derivatives. These are terpene compounds containing the abscisic acid moiety, which is characterized by a 3-methylpenta-2,4-dienoic acid attached to the C1 carbon of a 4-oxocyclohex-2-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Abscisic acids and derivatives

Alternative Parents

Substituents

Abscisic acid
Medium-chain fatty acid
Branched fatty acid
Cyclohexenone
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Tertiary alcohol
Cyclic ketone
Ketone
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Carbonyl group
Organic oxide
Primary alcohol
Organooxygen compound
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	0.84	ALOGPS
logP	0.81	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	4.6	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.75 m³·mol⁻¹	ChemAxon
Polarizability	29.2 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

HMDB0036094

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014934

KNApSAcK ID

C00011540

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131751913

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Nigellic acid (NP0048449)

MOL for NP0048449 (Nigellic acid)

3D MOL for NP0048449 (Nigellic acid)

3D SDF for NP0048449 (Nigellic acid)

3D-SDF for NP0048449 (Nigellic acid)

PDB for NP0048449 (Nigellic acid)

3D PDB for NP0048449 (Nigellic acid)

SMILES for NP0048449 (Nigellic acid)

INCHI for NP0048449 (Nigellic acid)

Structure for NP0048449 (Nigellic acid)

3D Structure for NP0048449 (Nigellic acid)