NP-MRD: Showing NP-Card for (3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one (NP0184951)

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Record Information

Version

1.0

Created at

2022-09-04 00:13:03 UTC

Updated at

2022-09-04 00:13:03 UTC

NP-MRD ID

NP0184951

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one

Description

(3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-1,2,3,6-tetrahydropyrazin-2-one 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. (3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one is found in Lamellodysidea herbacea. Based on a literature review very few articles have been published on (3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-1,2,3,6-tetrahydropyrazin-2-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309042202132D          

 23 23  0  0  1  0            999 V2000
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  1  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  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  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  2  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   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 Cl  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    3.3000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    3.3000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  4 18  1  0  0  0  0
 18 19  1  0  0  0  0
  2 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0184951

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](C[C@@H]1N=C(O)\C(=C/[C@H](C)C(Cl)(Cl)Cl)N(C)C1=O)C(Cl)(Cl)Cl

> <INCHI_IDENTIFIER>
InChI=1S/C13H16Cl6N2O2/c1-6(12(14,15)16)4-8-11(23)21(3)9(10(22)20-8)5-7(2)13(17,18)19/h5-8H,4H2,1-3H3,(H,20,22)/b9-5+/t6-,7-,8-/m0/s1

> <INCHI_KEY>
SQXOACQRLIPUKW-HSWZZFRHSA-N

> <FORMULA>
C13H16Cl6N2O2

> <MOLECULAR_WEIGHT>
444.98

> <EXACT_MASS>
441.934294

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
39.328076370576795

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-1,2,3,6-tetrahydropyrazin-2-one

> <JCHEM_LOGP>
4.093103340000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.254755453960295

> <JCHEM_PKA_STRONGEST_BASIC>
0.15044694772367417

> <JCHEM_POLAR_SURFACE_AREA>
52.900000000000006

> <JCHEM_REFRACTIVITY>
99.65349999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-3H-pyrazin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   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   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.000  -3.080   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  -4.620   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0      -0.000  -6.160   0.000  0.00  0.00          Cl+0
HETATM   14 Cl   UNK     0       1.540  -4.620   0.000  0.00  0.00          Cl+0
HETATM   15 Cl   UNK     0      -1.540  -4.620   0.000  0.00  0.00          Cl+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0       2.667   7.700   0.000  0.00  0.00          Cl+0
HETATM   22 Cl   UNK     0       4.207   6.160   0.000  0.00  0.00          Cl+0
HETATM   23 Cl   UNK     0       1.127   6.160   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16    8   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    4   19                                                  
CONECT   19   18                                                            
CONECT   20    2   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₆Cl₆N₂O₂

Average Mass

444.9800 Da

Monoisotopic Mass

441.93429 Da

IUPAC Name

(3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-1,2,3,6-tetrahydropyrazin-2-one

Traditional Name

(3S,6E)-5-hydroxy-1-methyl-3-[(2S)-3,3,3-trichloro-2-methylpropyl]-6-[(2S)-3,3,3-trichloro-2-methylpropylidene]-3H-pyrazin-2-one

CAS Registry Number

Not Available

SMILES

C[C@@H](C[C@@H]1N=C(O)\C(=C/[C@H](C)C(Cl)(Cl)Cl)N(C)C1=O)C(Cl)(Cl)Cl

InChI Identifier

InChI=1S/C13H16Cl6N2O2/c1-6(12(14,15)16)4-8-11(23)21(3)9(10(22)20-8)5-7(2)13(17,18)19/h5-8H,4H2,1-3H3,(H,20,22)/b9-5+/t6-,7-,8-/m0/s1

InChI Key

SQXOACQRLIPUKW-HSWZZFRHSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Lamellodysidea herbacea	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
N-methylpiperazine
N-alkylpiperazine
1,4-diazinane
Piperazine
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Carboxamide group
Lactam
Organoheterocyclic compound
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organochloride
Organohalogen compound
Organooxygen compound
Organic oxygen compound
Alkyl chloride
Carbonyl group
Organic nitrogen compound
Alkyl halide
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	4.09	ChemAxon
pKa (Strongest Acidic)	5.25	ChemAxon
pKa (Strongest Basic)	0.15	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	52.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	99.65 m³·mol⁻¹	ChemAxon
Polarizability	39.33 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

10232714

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15344844

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one (NP0184951)

MOL for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

3D MOL for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

3D SDF for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

3D-SDF for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

PDB for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

3D PDB for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

SMILES for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

INCHI for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

Structure for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)

3D Structure for NP0184951 ((3s,6e)-5-hydroxy-1-methyl-3-[(2s)-3,3,3-trichloro-2-methylpropyl]-6-[(2s)-3,3,3-trichloro-2-methylpropylidene]-3h-pyrazin-2-one)