NP-MRD: Showing NP-Card for 3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one (NP0234156)

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Record Information

Version

2.0

Created at

2022-09-06 16:02:15 UTC

Updated at

2022-09-06 16:02:15 UTC

NP-MRD ID

NP0234156

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one

Description

3-Benzyl-5-hydroxy-6-[(1H-indol-3-yl)methyl]-1-methyl-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. 3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one is found in Streptomyces ipomoeae. 3-Benzyl-5-hydroxy-6-[(1H-indol-3-yl)methyl]-1-methyl-1,2,3,6-tetrahydropyrazin-2-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004151514112D          

 26 29  0  0  0  0            999 V2000
   -0.2203   -0.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -3.2777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -2.6646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441   -2.8361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961   -2.2230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7031   -2.3945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2551   -1.7814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0002   -0.9968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1932   -0.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6412   -1.4384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -1.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -1.2669    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
  3  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
  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
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  5 13  1  0  0  0  0
  8 13  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  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
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
 17 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END


  Mrv1533004151514112D          

 26 29  0  0  0  0            999 V2000
   -0.2203   -0.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -3.2777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -2.6646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441   -2.8361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961   -2.2230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7031   -2.3945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2551   -1.7814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0002   -0.9968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1932   -0.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6412   -1.4384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -1.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -1.2669    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
  3  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
  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
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  5 13  1  0  0  0  0
  8 13  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  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
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
 17 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0234156

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C(CC2=CNC3=CC=CC=C23)C(=O)NC(CC2=CC=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H21N3O2/c1-24-19(12-15-13-22-17-10-6-5-9-16(15)17)20(25)23-18(21(24)26)11-14-7-3-2-4-8-14/h2-10,13,18-19,22H,11-12H2,1H3,(H,23,25)

> <INCHI_KEY>
XTHCOAZHAYZMDV-UHFFFAOYSA-N

> <FORMULA>
C21H21N3O2

> <MOLECULAR_WEIGHT>
347.418

> <EXACT_MASS>
347.163376928

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
36.17764736777775

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-benzyl-6-[(1H-indol-3-yl)methyl]-1-methylpiperazine-2,5-dione

> <ALOGPS_LOGP>
2.68

> <JCHEM_LOGP>
2.5620527993333324

> <ALOGPS_LOGS>
-3.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.15137876492073

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.446046764497913

> <JCHEM_PKA_STRONGEST_BASIC>
-4.270047557987975

> <JCHEM_POLAR_SURFACE_AREA>
65.2

> <JCHEM_REFRACTIVITY>
99.816

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.96e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-benzyl-6-(1H-indol-3-ylmethyl)-1-methylpiperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         0                                  
HETATM    1  C   UNK     0      -0.411  -1.724   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -0.887  -3.189   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.333  -5.798   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.698  -6.943   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0      -1.839  -6.118   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -2.869  -4.974   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.376  -5.294   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.406  -4.150   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -6.912  -4.470   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -7.943  -3.325   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -7.467  -1.861   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.961  -1.541   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.930  -2.685   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.393  -3.509   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.424  -2.365   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5    8                                                  
CONECT   14    3   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25   17    2   26                                                  
CONECT   26   25                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₁N₃O₂

Average Mass

347.4180 Da

Monoisotopic Mass

347.16338 Da

IUPAC Name

3-benzyl-6-[(1H-indol-3-yl)methyl]-1-methylpiperazine-2,5-dione

Traditional Name

3-benzyl-6-(1H-indol-3-ylmethyl)-1-methylpiperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

CN1C(CC2=CNC3=CC=CC=C23)C(=O)NC(CC2=CC=CC=C2)C1=O

InChI Identifier

InChI=1S/C21H21N3O2/c1-24-19(12-15-13-22-17-10-6-5-9-16(15)17)20(25)23-18(21(24)26)11-14-7-3-2-4-8-14/h2-10,13,18-19,22H,11-12H2,1H3,(H,23,25)

InChI Key

XTHCOAZHAYZMDV-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces ipomoeae	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
3-alkylindole
Indole
Indole or derivatives
Dioxopiperazine
2,5-dioxopiperazine
N-methylpiperazine
N-alkylpiperazine
Monocyclic benzene moiety
1,4-diazinane
Piperazine
Substituted pyrrole
Benzenoid
Tertiary carboxylic acid amide
Pyrrole
Heteroaromatic compound
Secondary carboxylic acid amide
Carboxamide group
Lactam
Organoheterocyclic compound
Azacycle
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	2.68	ALOGPS
logP	2.56	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	11.45	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.2 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	99.82 m³·mol⁻¹	ChemAxon
Polarizability	36.18 Å³	ChemAxon
Number of Rings	4	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one (NP0234156)

MOL for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

3D MOL for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

3D SDF for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

3D-SDF for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

PDB for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

3D PDB for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

SMILES for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

INCHI for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

Structure for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)

3D Structure for NP0234156 (3-benzyl-5-hydroxy-6-(1h-indol-3-ylmethyl)-1-methyl-3,6-dihydropyrazin-2-one)