NP-MRD: Showing NP-Card for 5C-aglycone (NP0087205)

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Record Information

Version

2.0

Created at

2022-05-11 16:43:01 UTC

Updated at

2022-05-11 16:43:01 UTC

NP-MRD ID

NP0087205

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5C-aglycone

Description

5C-aglycone belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position. 5C-aglycone was first documented in 2005 (PMID: 15722567). 5C-aglycone is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    0.1254   -2.7663    0.2711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9197   -1.4900    0.1753 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3664   -0.3171    0.4235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0474   -0.2599    0.7991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8870    0.5493   -0.1513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3449    0.6151    0.2297 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1316    1.4643   -0.7649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0093   -0.6965    0.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4072   -1.7142   -0.1059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3010   -0.7851    0.7688 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1735    0.8945    0.3187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6799    2.0403    0.5489 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5875    0.8777   -0.0533 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3337    2.0362   -0.1468 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6639    1.9497   -0.5029 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2162    0.7090   -0.7569 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5015   -0.4574   -0.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1617   -0.3515   -0.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3319   -1.5305   -0.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8890   -2.6474   -0.4427 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1354   -2.9810    1.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7518   -2.6928   -0.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7607   -3.5897   -0.0586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4225   -1.2873    0.9404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0922    0.1868    1.8418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8671   -0.0045   -1.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4737    1.5333   -0.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4954    1.0987    1.2245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9766    1.9588   -0.2417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5656    0.8015   -1.5195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5057    2.2790   -1.1826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5746   -0.4929    1.6969 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8442    2.9838    0.0650 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2592    2.8494   -0.5797 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2648    0.6677   -1.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9099   -1.4309   -0.8651 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 19  1  0
 19 20  2  0
 19 18  1  0
 18 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 13 11  1  0
 11 12  2  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
 11  3  1  0
 17 18  1  0
  7 29  1  0
  7 30  1  0
  7 31  1  0
  6 28  1  1
  5 26  1  0
  5 27  1  0
  4 24  1  0
  4 25  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 10 32  1  0
M  END

7C-aglycone.mol
  Mrv0541 02231219592D          

 20 21  0  0  0  0            999 V2000
   -1.0717    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  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
  1 10  1  0  0  0  0
  5 10  2  0  0  0  0
  4 11  2  0  0  0  0
  1 12  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 15 17  1  0  0  0  0
  3 13  1  0  0  0  0
  2 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0087205

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H16O4/c1-9(16(19)20)7-8-11-10(2)14(17)12-5-3-4-6-13(12)15(11)18/h3-6,9H,7-8H2,1-2H3,(H,19,20)

> <INCHI_KEY>
ALLYVKRLOHDVKI-UHFFFAOYSA-N

> <FORMULA>
C16H16O4

> <MOLECULAR_WEIGHT>
272.2958

> <EXACT_MASS>
272.104859

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
28.592988100054306

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoic acid

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
2.8418694376666664

> <ALOGPS_LOGS>
-3.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9053555081283307

> <JCHEM_PKA_STRONGEST_BASIC>
-7.215270896918987

> <JCHEM_POLAR_SURFACE_AREA>
71.44

> <JCHEM_REFRACTIVITY>
74.9403

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.76e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5c-aglycone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 7C-aglycone.mol                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.001   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.667   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.667  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.668  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.002  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.002   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.668   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.334   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.001  -3.080   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.001   3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.667  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.334  -1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.334  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.668   0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.002  -1.540   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2   10   12                                                  
CONECT    2    1    3   20                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    1    5                                                  
CONECT   11    4                                                            
CONECT   12    1                                                            
CONECT   13   14    3                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   18   19   15                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Value	Source
1,4-Dihydro-a,3-dimethyl-1,4-dioxo-2-naphthalenebutanoate	HMDB
1,4-Dihydro-a,3-dimethyl-1,4-dioxo-2-naphthalenebutanoic acid	HMDB
2-Methyl-3-(3'-3'-carboxymethylpropyl)-1,4-naphthoquinone	HMDB
2-Methyl-3-(3'-carboxy-3'-methylpropyl)-1,4-naphthoquinone	HMDB
2-Methyl-3-(3'-carboxybutyl)-1,4-naphthoquinone	HMDB
2-Methyl-3-(3-carboxybutyl)-1,4-naphthoquinone	HMDB
Phylloquinone aglycone II	HMDB
Vitamin K1 aglycone II	HMDB
2-Methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoate	HMDB

Chemical Formula

C₁₆H₁₆O₄

Average Mass

272.2958 Da

Monoisotopic Mass

272.10486 Da

IUPAC Name

2-methyl-4-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)butanoic acid

Traditional Name

5c-aglycone

CAS Registry Number

Not Available

SMILES

CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O

InChI Identifier

InChI=1S/C16H16O4/c1-9(16(19)20)7-8-11-10(2)14(17)12-5-3-4-6-13(12)15(11)18/h3-6,9H,7-8H2,1-2H3,(H,19,20)

InChI Key

ALLYVKRLOHDVKI-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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Quinone and hydroquinone lipids

Direct Parent

Vitamin K compounds

Alternative Parents

Substituents

Naphthoquinone
Naphthalene
Aryl ketone
Quinone
Benzenoid
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic 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	2.38	ALOGPS
logP	2.84	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	3.91	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	71.44 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	74.94 m³·mol⁻¹	ChemAxon
Polarizability	28.59 Å³	ChemAxon
Number of Rings	2	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

HMDB0004810

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB023421

KNApSAcK ID

Not Available

Chemspider ID

2339843

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

7074

PubChem Compound

3082405

PDB ID

Not Available

ChEBI ID

89486

Good Scents ID

Not Available

References

General References

Harrington DJ, Soper R, Edwards C, Savidge GF, Hodges SJ, Shearer MJ: Determination of the urinary aglycone metabolites of vitamin K by HPLC with redox-mode electrochemical detection. J Lipid Res. 2005 May;46(5):1053-60. Epub 2005 Feb 1. [PubMed:15722567 ]

Showing NP-Card for 5C-aglycone (NP0087205)

MOL for NP0087205 (5C-aglycone)

3D MOL for NP0087205 (5C-aglycone)

3D SDF for NP0087205 (5C-aglycone)

3D-SDF for NP0087205 (5C-aglycone)

PDB for NP0087205 (5C-aglycone)

3D PDB for NP0087205 (5C-aglycone)

SMILES for NP0087205 (5C-aglycone)

INCHI for NP0087205 (5C-aglycone)

Structure for NP0087205 (5C-aglycone)

3D Structure for NP0087205 (5C-aglycone)