NP-MRD: Showing NP-Card for 3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol (NP0327165)

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Record Information

Version

2.0

Created at

2022-09-12 09:28:18 UTC

Updated at

2022-09-12 09:28:18 UTC

NP-MRD ID

NP0327165

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol

Description

3,6-Dibenzyl-3,6-dihydropyrazine-2,5-diol belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. 3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol is found in Epicoccum nigrum. 3,6-Dibenzyl-3,6-dihydropyrazine-2,5-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 42  0  0  0  0  0  0  0  0999 V2000
    2.1421   -1.6143    1.3360 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1433   -0.9177    1.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1078   -1.5503    0.8747 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3509   -0.8405    0.9232 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0474   -1.0308   -0.4103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3407   -0.3423   -0.4755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5001   -0.9875   -0.0855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7359   -0.3725   -0.1326 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7749    0.9291   -0.5896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6164    1.5711   -0.9784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822    0.9565   -0.9312 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2347    0.5562    1.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2462    1.1438    1.8416 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0023    1.2272    1.1400 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2389    0.5340    0.9541 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9275    0.9193   -0.3456 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3010    0.3605   -0.4114 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3429    1.1375    0.0965 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6367    0.6689    0.0614 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9321   -0.5582   -0.4669 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9121   -1.3379   -0.9729 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6087   -0.8640   -0.9366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1363   -2.5725    0.6881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9840   -1.3593    1.7015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3868   -0.6734   -1.2074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1516   -2.1371   -0.5517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4946   -2.0205    0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6508   -0.8816    0.1752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7308    1.4512   -0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6621    2.6101   -1.3412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4901    1.4983   -1.2475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0222    2.2697    1.1355 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9335    0.8870    1.7719 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3342    0.5734   -1.2259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0083    2.0198   -0.4446 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1599    2.1116    0.5231 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4272    1.3017    0.4668 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9721   -0.8914   -0.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1751   -2.3043   -1.3846 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8042   -1.4710   -1.3321 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  4 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 15  2  1  0
 22 17  1  0
 11  6  1  0
  3 23  1  0
  4 24  1  1
  5 25  1  0
  5 26  1  0
  7 27  1  0
  8 28  1  0
  9 29  1  0
 10 30  1  0
 11 31  1  0
 14 32  1  0
 15 33  1  1
 16 34  1  0
 16 35  1  0
 18 36  1  0
 19 37  1  0
 20 38  1  0
 21 39  1  0
 22 40  1  0
M  END


  Mrv1533004161518392D          

 22 24  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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
    0.7145   -0.4125    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
    0.0000    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
    1.4289    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
  1  2  2  0  0  0  0
  2  3  1  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
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
  4 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 17 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0327165

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1NC(CC2=CC=CC=C2)C(=O)NC1CC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H18N2O2/c21-17-15(11-13-7-3-1-4-8-13)19-18(22)16(20-17)12-14-9-5-2-6-10-14/h1-10,15-16H,11-12H2,(H,19,22)(H,20,21)

> <INCHI_KEY>
JUAPMRSLDANLAS-UHFFFAOYSA-N

> <FORMULA>
C18H18N2O2

> <MOLECULAR_WEIGHT>
294.354

> <EXACT_MASS>
294.136827828

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
30.001128919101326

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,6-dibenzylpiperazine-2,5-dione

> <ALOGPS_LOGP>
1.66

> <JCHEM_LOGP>
2.239614740666666

> <ALOGPS_LOGS>
-4.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.116762062230956

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.0522124941073

> <JCHEM_PKA_STRONGEST_BASIC>
-4.450961548272949

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
83.83280000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,6-dibenzylpiperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.335  -3.080   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       2.667  -4.620   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    4   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    2   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₈N₂O₂

Average Mass

294.3540 Da

Monoisotopic Mass

294.13683 Da

IUPAC Name

3,6-dibenzylpiperazine-2,5-dione

Traditional Name

3,6-dibenzylpiperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

O=C1NC(CC2=CC=CC=C2)C(=O)NC1CC1=CC=CC=C1

InChI Identifier

InChI=1S/C18H18N2O2/c21-17-15(11-13-7-3-1-4-8-13)19-18(22)16(20-17)12-14-9-5-2-6-10-14/h1-10,15-16H,11-12H2,(H,19,22)(H,20,21)

InChI Key

JUAPMRSLDANLAS-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
Epicoccum nigrum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Dioxopiperazine
2,5-dioxopiperazine
Monocyclic benzene moiety
1,4-diazinane
Piperazine
Benzenoid
Secondary carboxylic acid amide
Lactam
Carboxamide group
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Carbonyl group
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
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	1.66	ALOGPS
logP	2.24	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	11.05	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.2 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	83.83 m³·mol⁻¹	ChemAxon
Polarizability	30 Å³	ChemAxon
Number of Rings	3	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

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

16829

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol (NP0327165)

MOL for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

3D MOL for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

3D SDF for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

3D-SDF for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

PDB for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

3D PDB for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

SMILES for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

INCHI for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

Structure for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)

3D Structure for NP0327165 (3,6-dibenzyl-3,6-dihydropyrazine-2,5-diol)