NP-MRD: Showing NP-Card for 3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one (NP0206780)

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Record Information

Version

2.0

Created at

2022-09-05 03:09:22 UTC

Updated at

2022-09-05 03:09:22 UTC

NP-MRD ID

NP0206780

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one

Description

3-(Cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,4H,10H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-1,2,3,6-tetrahydropyrazin-2-one belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom. Based on a literature review very few articles have been published on 3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,4H,10H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-1,2,3,6-tetrahydropyrazin-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052205092D          

 38 43  0  0  0  0            999 V2000
    2.4860    2.1236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

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M  END


  Mrv1652309052205092D          

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   -1.9614    1.7117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1544    1.5402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595    1.1971    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665    1.0256    0.0000 C   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  1  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 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  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 30 37  1  0  0  0  0
 37 38  1  0  0  0  0
 26 38  1  0  0  0  0
  2 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0206780

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(CC2N(O)C(=O)C(CC3CCCCC3)N=C2O)C2NC(CC(=O)N2C2=CC=CC=C12)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H36N4O4/c1-30(18-25-27(36)31-23(28(37)34(25)38)16-19-10-4-2-5-11-19)21-14-8-9-15-24(21)33-26(35)17-22(32-29(30)33)20-12-6-3-7-13-20/h3,6-9,12-15,19,22-23,25,29,32,38H,2,4-5,10-11,16-18H2,1H3,(H,31,36)

> <INCHI_KEY>
SYRKXVJXAYRATF-UHFFFAOYSA-N

> <FORMULA>
C30H36N4O4

> <MOLECULAR_WEIGHT>
516.642

> <EXACT_MASS>
516.273655655

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
56.601829182659884

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,4H,10H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-1,2,3,6-tetrahydropyrazin-2-one

> <JCHEM_LOGP>
2.7133214675825568

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.918037579152579

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.071988902204189

> <JCHEM_PKA_STRONGEST_BASIC>
5.933725589993093

> <JCHEM_POLAR_SURFACE_AREA>
105.47

> <JCHEM_REFRACTIVITY>
142.1766

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one

> <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       4.640   3.964   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.610   2.820   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.580   3.964   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.055   5.429   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.025   6.573   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.519   6.253   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.501   8.038   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       4.007   8.358   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.483   9.823   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.989  10.143   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.465  11.607   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.972  11.928   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.002  10.783   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.526   9.319   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.020   8.998   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.038   7.214   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.544   7.534   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       4.562   5.749   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       5.592   4.604   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.856   1.914   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.362   2.235   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.393   1.090   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.917  -0.374   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.410  -0.695   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.380   0.450   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       2.840   0.450   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       1.810  -0.695   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.285  -2.159   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.303  -0.374   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.173   1.090   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.679   1.410   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.709   0.266   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.216   0.586   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.692   2.051   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -3.661   3.195   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.155   2.875   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       0.858   2.235   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       2.364   1.914   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   20   38                                             
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   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16    8   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    4   19                                                  
CONECT   19   18                                                            
CONECT   20    2   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   20   26                                                  
CONECT   26   25   27   38                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31   37                                                  
CONECT   31   30   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   30   38                                                       
CONECT   38   37   26    2                                                  
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₆N₄O₄

Average Mass

516.6420 Da

Monoisotopic Mass

516.27366 Da

IUPAC Name

3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,4H,10H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-1,2,3,6-tetrahydropyrazin-2-one

Traditional Name

3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1H,2H,3H,10aH-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one

CAS Registry Number

Not Available

SMILES

CC1(CC2N(O)C(=O)C(CC3CCCCC3)N=C2O)C2NC(CC(=O)N2C2=CC=CC=C12)C1=CC=CC=C1

InChI Identifier

InChI=1S/C30H36N4O4/c1-30(18-25-27(36)31-23(28(37)34(25)38)16-19-10-4-2-5-11-19)21-14-8-9-15-24(21)33-26(35)17-22(32-29(30)33)20-12-6-3-7-13-20/h3,6-9,12-15,19,22-23,25,29,32,38H,2,4-5,10-11,16-18H2,1H3,(H,31,36)

InChI Key

SYRKXVJXAYRATF-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Alpha-amino acid or derivatives
Indole or derivatives
2,5-dioxopiperazine
Dioxopiperazine
Benzenoid
Piperazine
1,4-diazinane
1,3-diazinane
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Secondary carboxylic acid amide
Lactam
Hydroxamic acid
Carboxamide group
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
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	2.71	ChemAxon
pKa (Strongest Acidic)	4.07	ChemAxon
pKa (Strongest Basic)	5.93	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	105.47 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	142.18 m³·mol⁻¹	ChemAxon
Polarizability	56.6 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

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

162991772

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one (NP0206780)

MOL for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

3D MOL for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

3D SDF for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

3D-SDF for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

PDB for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

3D PDB for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

SMILES for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

INCHI for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

Structure for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)

3D Structure for NP0206780 (3-(cyclohexylmethyl)-1,5-dihydroxy-6-({10-methyl-4-oxo-2-phenyl-1h,2h,3h,10ah-pyrimido[1,2-a]indol-10-yl}methyl)-3,6-dihydropyrazin-2-one)