NP-MRD: Showing NP-Card for 2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate (NP0280470)

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Record Information

Version

2.0

Created at

2022-09-09 06:16:58 UTC

Updated at

2022-09-09 06:16:58 UTC

NP-MRD ID

NP0280470

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate

Description

Pulcherriminic acid, also known as pulcherriminate, belongs to the class of organic compounds known as pyrazinium compounds. These are organic aromatic compounds containing a pyriazinium ring. 2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate is found in Metschnikowia pulcherrima. 2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate was first documented in 2020 (PMID: 33260656). Based on a literature review a small amount of articles have been published on Pulcherriminic acid (PMID: 34579848) (PMID: 34517294) (PMID: 32780266).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 38  0  0  0  0  0  0  0  0999 V2000
    4.9892    0.2334    0.7058 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6488    0.0395   -0.0212 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6720   -1.3588   -0.5461 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5769    0.3744    0.9500 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1947    0.2587    0.4607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666   -0.9490    0.3910 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1816   -2.1184    0.7944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7111   -1.0155   -0.0889 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.3451   -2.2262   -0.1607 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.3626    0.0829   -0.4931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7500    0.0119   -1.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7666    0.4969   -0.0140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7622   -0.3020    1.2688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1342    0.3705   -0.6514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7066    1.2920   -0.4119 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3019    2.3461   -0.7878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5585    1.3769    0.0603 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1672    2.6279    0.1176 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7517   -0.3268    0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9567   -0.1885    1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2973    1.2952    0.6741 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6733    0.7420   -0.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6156   -1.4328   -1.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8626   -1.5974   -1.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8328   -2.0947    0.2436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7980    1.4325    1.2980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7449   -0.2256    1.8765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1167   -2.9194    0.1657 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0349   -1.0369   -1.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8555    0.6109   -1.9229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5612    1.5626    0.2498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7633   -0.1105    1.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6996   -1.3722    1.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9883    0.0440    1.9839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0787   -0.1252   -1.6611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6153    1.3615   -0.7408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8249   -0.2676   -0.0563 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0569    3.1078    1.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 10 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 17  5  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  0
  3 23  1  0
  3 24  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  7 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  0
 13 32  1  0
 13 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 14 37  1  0
 18 38  1  0
M  CHG  2   8   1   9  -1
M  END


  Mrv1652309092208172D          

 18 18  0  0  0  0            999 V2000
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  5  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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    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
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  CHG  2   8   1   9  -1
M  END
> <DATABASE_ID>
NP0280470

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC1=C(O)[N+]([O-])=C(CC(C)C)C(=O)N1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H20N2O4/c1-7(2)5-9-11(15)14(18)10(6-8(3)4)12(16)13(9)17/h7-8,15,17H,5-6H2,1-4H3

> <INCHI_KEY>
BUHPPQFOKKRDPX-UHFFFAOYSA-N

> <FORMULA>
C12H20N2O4

> <MOLECULAR_WEIGHT>
256.302

> <EXACT_MASS>
256.142307132

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
26.699204231571773

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,6-dihydroxy-2,5-bis(2-methylpropyl)-3-oxo-3,4-dihydropyrazin-1-ium-1-olate

> <JCHEM_LOGP>
-0.7636826774717463

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.371015554991171

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.984337355726662

> <JCHEM_PKA_STRONGEST_BASIC>
-6.226488506653774

> <JCHEM_POLAR_SURFACE_AREA>
86.84

> <JCHEM_REFRACTIVITY>
78.84039999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+1
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   10   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    5   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
Pulcherriminate	Generator
2,5-Diisobutyl-3,6-dihydroxy-pyrazine-1,4-dioxide	MeSH

Chemical Formula

C₁₂H₂₀N₂O₄

Average Mass

256.3020 Da

Monoisotopic Mass

256.14231 Da

IUPAC Name

4,6-dihydroxy-2,5-bis(2-methylpropyl)-3-oxo-3,4-dihydropyrazin-1-ium-1-olate

Traditional Name

2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate

CAS Registry Number

Not Available

SMILES

CC(C)CC1=C(O)[N+]([O-])=C(CC(C)C)C(=O)N1O

InChI Identifier

InChI=1S/C12H20N2O4/c1-7(2)5-9-11(15)14(18)10(6-8(3)4)12(16)13(9)17/h7-8,15,17H,5-6H2,1-4H3

InChI Key

BUHPPQFOKKRDPX-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, 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
Metschnikowia pulcherrima	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazinium compounds. These are organic aromatic compounds containing a pyriazinium ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazinium compounds

Direct Parent

Pyrazinium compounds

Alternative Parents

Substituents

Pyrazinium
Pyrazine
Heteroaromatic compound
Lactam
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organic zwitterion
Organooxygen compound
Organonitrogen compound
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	-0.76	ChemAxon
pKa (Strongest Acidic)	2.98	ChemAxon
pKa (Strongest Basic)	-6.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	86.84 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	78.84 m³·mol⁻¹	ChemAxon
Polarizability	26.7 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

2340835

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3083664

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wang S, Zhang H, Qi T, Deng L, Yi L, Zeng K: Influence of arginine on the biocontrol efficiency of Metschnikowia citriensis against Geotrichum citri-aurantii causing sour rot of postharvest citrus fruit. Food Microbiol. 2022 Feb;101:103888. doi: 10.1016/j.fm.2021.103888. Epub 2021 Aug 26. [PubMed:34579848 ]
Wang S, Zhang H, Ruan C, Yi L, Deng L, Zeng K: Metschnikowia citriensis FL01 antagonize Geotrichum citri-aurantii in citrus fruit through key action of iron depletion. Int J Food Microbiol. 2021 Nov 2;357:109384. doi: 10.1016/j.ijfoodmicro.2021.109384. Epub 2021 Sep 7. [PubMed:34517294 ]
Yuan S, Yong X, Zhao T, Li Y, Liu J: Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid in Bacillus. Molecules. 2020 Nov 28;25(23):5611. doi: 10.3390/molecules25235611. [PubMed:33260656 ]
Melvydas V, Svediene J, Skridlaite G, Vaiciuniene J, Garjonyte R: In vitro inhibition of Saccharomyces cerevisiae growth by Metschnikowia spp. triggered by fast removal of iron via two ways. Braz J Microbiol. 2020 Dec;51(4):1953-1964. doi: 10.1007/s42770-020-00357-3. Epub 2020 Aug 11. [PubMed:32780266 ]
LOTUS database [Link]

Showing NP-Card for 2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate (NP0280470)

MOL for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

3D MOL for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

3D SDF for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

3D-SDF for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

PDB for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

3D PDB for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

SMILES for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

INCHI for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

Structure for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)

3D Structure for NP0280470 (2,4-dihydroxy-3,6-bis(2-methylpropyl)-5-oxopyrazin-1-ium-1-olate)