NP-MRD: Showing NP-Card for 3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate) (NP0218293)

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Record Information

Version

2.0

Created at

2022-09-05 18:54:42 UTC

Updated at

2022-09-05 18:54:42 UTC

NP-MRD ID

NP0218293

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate)

Description

Pulcherriminate(2-), also known as pulcherriminic acid, belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms. Pulcherriminate(2-) is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. 3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate) is found in Caesalpinia pulcherrima. 3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate) was first documented in 1965 (PMID: 5837792). Based on a literature review a significant number of articles have been published on pulcherriminate(2-) (PMID: 20690619) (PMID: 4204912) (PMID: 4778264) (PMID: 4985560) (PMID: 5923137).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052220542D          

 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  5  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  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
    0.7145   -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  5  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  5  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  2  0  0  0  0
  8 10  1  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  2  0  0  0  0
 15 16  1  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  4   7  -1   8   1  16  -1  18  -1
M  END
> <DATABASE_ID>
NP0218293

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC1=C([O-])[N+](=O)C(CC(C)C)=C([O-])N1[O-]

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

> <INCHI_KEY>
WXWWNANFOZVVLD-UHFFFAOYSA-L

> <FORMULA>
C12H18N2O4

> <MOLECULAR_WEIGHT>
254.287

> <EXACT_MASS>
254.127754227

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.20900586234298

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,6-bis(2-methylpropyl)-1-oxo-1,4-dihydro-1lambda5-pyrazin-1-ylium-2,4,5-tris(olate)

> <JCHEM_LOGP>
2.3573130446666672

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.528367089007946

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8072633424533437

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3231130760872585

> <JCHEM_POLAR_SURFACE_AREA>
92.5

> <JCHEM_REFRACTIVITY>
97.51790000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3,6-bis(2-methylpropyl)-1-oxo-1H-1lambda5-pyrazin-1-ylium-2,4,5-tris(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-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-1
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+0
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-1
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-1
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
Pulcherriminic acid	ChEBI
Pulcherriminic acid(2-)	ChEBI
Pulcherriminate	Generator

Chemical Formula

C₁₂H₁₈N₂O₄

Average Mass

254.2870 Da

Monoisotopic Mass

254.12775 Da

IUPAC Name

3,6-bis(2-methylpropyl)-1-oxo-1,4-dihydro-1lambda5-pyrazin-1-ylium-2,4,5-tris(olate)

Traditional Name

3,6-bis(2-methylpropyl)-1-oxo-1H-1lambda5-pyrazin-1-ylium-2,4,5-tris(olate)

CAS Registry Number

Not Available

SMILES

CC(C)CC1=C([O-])[N+](=O)C(CC(C)C)=C([O-])N1[O-]

InChI Identifier

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

InChI Key

WXWWNANFOZVVLD-UHFFFAOYSA-L

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
Caesalpinia pulcherrima	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazines. Pyrazines are compounds containing a pyrazine ring, which is a six-member aromatic heterocycle, that consists of two nitrogen atoms (at positions 1 and 4) and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrazines

Direct Parent

Pyrazines

Alternative Parents

Substituents

Pyrazine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organic anion (CHEBI:77663 )

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	2.36	ChemAxon
pKa (Strongest Acidic)	1.81	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	92.5 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	97.52 m³·mol⁻¹	ChemAxon
Polarizability	26.21 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

31150355

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

77663

Good Scents ID

Not Available

References

General References

Cryle MJ, Bell SG, Schlichting I: Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase. Biochemistry. 2010 Aug 31;49(34):7282-96. doi: 10.1021/bi100910y. [PubMed:20690619 ]
Uffen RL, Canale-Parola E: Synthesis of pulcherriminic acid by Bacillus subtilis. J Bacteriol. 1972 Jul;111(1):86-93. doi: 10.1128/jb.111.1.86-93.1972. [PubMed:4204912 ]
Plattner H, Diekmann H: [Metabolic products of microorganisms. 124. Incorporation of L-leucine in cyclo-L-leucyl-L-leucyl, the intermediate in the biosynthesis of pulcherriminic acid, in cell-free extracts from Candida pulcherrima (author's transl)]. Arch Mikrobiol. 1973 Nov 19;93(4):363-5. [PubMed:4778264 ]
Uffen RL, Canale-Parola E: Isolation of pulcherriminic acid from cultures of Bacillus cereus var. alesti. Z Allg Mikrobiol. 1969;9(3):231-3. [PubMed:4985560 ]
MacDonald JC: Biosynthesis of pulcherriminic acid. Biochem J. 1965 Aug;96(2):533-8. doi: 10.1042/bj0960533. [PubMed:5837792 ]
MacDonald JC: The isolation of pulcherriminic acid from Micrococcus violagabriellae. Can J Microbiol. 1966 Feb;12(1):55-9. doi: 10.1139/m66-009. [PubMed:5923137 ]
LOTUS database [Link]

Showing NP-Card for 3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate) (NP0218293)

MOL for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

3D MOL for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

3D SDF for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

3D-SDF for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

PDB for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

3D PDB for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

SMILES for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

INCHI for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

Structure for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))

3D Structure for NP0218293 (3,6-bis(2-methylpropyl)-1-oxo-1h-1λ⁵-pyrazin-1-ylium-2,4,5-tris(olate))