NP-MRD: Showing NP-Card for 2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one (NP0234712)

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Record Information

Version

2.0

Created at

2022-09-06 16:55:18 UTC

Updated at

2022-09-06 16:55:18 UTC

NP-MRD ID

NP0234712

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one

Description

2-(Ethylimino)-5-[(1H-indol-3-yl)methylidene]-1,3-dimethylimidazolidin-4-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. 2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one is found in Hymeniacidon perlevis. 2-(Ethylimino)-5-[(1H-indol-3-yl)methylidene]-1,3-dimethylimidazolidin-4-one is a moderately basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
    6.0421    0.9061    0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8394    0.1325   -0.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6398    0.7500   -0.0917 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609    0.2383   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0231   -1.0396   -0.5032 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8540   -2.0928   -1.0521 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6179   -1.1278   -0.2932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0622   -2.1572   -0.5700 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1425    0.1186    0.2640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0672    0.4625    0.6278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2575   -0.3679    0.5549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -1.6634    0.9394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7890   -1.9924    0.6349 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4057   -0.9566    0.0628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7002   -0.7774   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0067    0.4447   -0.9575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1035    1.4549   -1.0229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8359    1.2577   -0.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4673    0.0634    0.0052 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2932    0.9422    0.3774 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3169    2.3025    0.8898 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2574    1.8133   -0.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9204    0.2347   -0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9156    1.2213    1.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9138    0.1929   -1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9913   -0.9137   -0.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3940   -2.6746   -0.2948 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5361   -1.7336   -1.8369 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1522   -2.8290   -1.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1875    1.4917    1.0326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7767   -2.3129    1.4272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2195   -2.9140    0.8246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4271   -1.5554   -0.3791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0078    0.6161   -1.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3396    2.4181   -1.4420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0961    2.0581   -0.5801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8867    3.0135    0.1460 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3463    2.6098    1.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7068    2.3653    1.8073 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  1  0
 20 21  1  0
 20  4  1  0
 19 11  1  0
 19 14  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  6 27  1  0
  6 28  1  0
  6 29  1  0
 10 30  1  0
 12 31  1  0
 13 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 21 37  1  0
 21 38  1  0
 21 39  1  0
M  END


  Mrv1533004251502332D          

 21 23  0  0  0  0            999 V2000
   -1.9284   -4.9998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3763   -4.3867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -3.6021    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -2.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508   -2.1820    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0044   -1.8464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5363   -1.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500   -0.9490    0.0000 O   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
   -0.2587   -3.0752    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538   -3.7897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  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  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  4  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 11 19  1  0  0  0  0
 14 19  1  0  0  0  0
  9 20  1  0  0  0  0
  4 20  1  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0234712

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCN=C1N(C)C(=O)C(=CC2=CNC3=CC=CC=C23)N1C

> <INCHI_IDENTIFIER>
InChI=1S/C16H18N4O/c1-4-17-16-19(2)14(15(21)20(16)3)9-11-10-18-13-8-6-5-7-12(11)13/h5-10,18H,4H2,1-3H3

> <INCHI_KEY>
WPOIHWRJVKWRCZ-UHFFFAOYSA-N

> <FORMULA>
C16H18N4O

> <MOLECULAR_WEIGHT>
282.347

> <EXACT_MASS>
282.148061216

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.677258369530193

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(ethylimino)-5-[(1H-indol-3-yl)methylidene]-1,3-dimethylimidazolidin-4-one

> <ALOGPS_LOGP>
2.53

> <JCHEM_LOGP>
1.9661624149999999

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.843305800329329

> <JCHEM_PKA_STRONGEST_BASIC>
2.7248331770785983

> <JCHEM_POLAR_SURFACE_AREA>
51.7

> <JCHEM_REFRACTIVITY>
84.70779999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(ethylimino)-5-(1H-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      -3.600  -9.333   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.569  -8.188   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -3.045  -6.724   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.015  -5.579   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.335  -4.073   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -3.742  -3.447   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.001  -3.303   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.840  -1.771   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -0.483  -5.740   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       0.287  -7.074   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   20                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   11   14                                                  
CONECT   20    9    4   21                                                  
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₈N₄O

Average Mass

282.3470 Da

Monoisotopic Mass

282.14806 Da

IUPAC Name

2-(ethylimino)-5-[(1H-indol-3-yl)methylidene]-1,3-dimethylimidazolidin-4-one

Traditional Name

2-(ethylimino)-5-(1H-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one

CAS Registry Number

Not Available

SMILES

CCN=C1N(C)C(=O)C(=CC2=CNC3=CC=CC=C23)N1C

InChI Identifier

InChI=1S/C16H18N4O/c1-4-17-16-19(2)14(15(21)20(16)3)9-11-10-18-13-8-6-5-7-12(11)13/h5-10,18H,4H2,1-3H3

InChI Key

WPOIHWRJVKWRCZ-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
Hymeniacidon perlevis	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
Indole
Indole or derivatives
Imidazolidinone
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Imidazolidine
Pyrrole
Guanidine
Organoheterocyclic compound
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
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	2.53	ALOGPS
logP	1.97	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	15.84	ChemAxon
pKa (Strongest Basic)	2.72	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.7 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	84.71 m³·mol⁻¹	ChemAxon
Polarizability	31.68 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

85107765

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one (NP0234712)

MOL for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

3D MOL for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

3D SDF for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

3D-SDF for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

PDB for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

3D PDB for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

SMILES for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

INCHI for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

Structure for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)

3D Structure for NP0234712 (2-(ethylimino)-5-(1h-indol-3-ylmethylidene)-1,3-dimethylimidazolidin-4-one)