NP-MRD: Showing NP-Card for dichotomide iii (NP0237707)

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Record Information

Version

2.0

Created at

2022-09-06 20:56:10 UTC

Updated at

2022-09-06 20:56:10 UTC

NP-MRD ID

NP0237707

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dichotomide iii

Description

Dichotomide III belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. Dichotomide III is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. dichotomide iii is found in Stellaria dichotoma. Based on a literature review very few articles have been published on dichotomide III.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 42  0  0  0  0  0  0  0  0999 V2000
    7.8615    0.6548   -0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4407    0.6210   -0.1446 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7131    0.6857    1.0514 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3985    0.7729    2.1065 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2722    0.6554    1.0872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5879    0.5633   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1620    0.5305   -0.0465 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4659   -0.5697   -0.5808 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1195   -1.5539   -1.0681 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0085   -0.6478   -0.6083 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7524    0.3774   -0.1001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1301    0.2959   -0.1299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7033   -0.8271   -0.6761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0313   -0.6380   -0.5736 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3014    0.5569    0.0140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4623    1.2224    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4576    2.4617    0.9562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2624    3.0876    1.2542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1005    2.4215    0.9191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1099    1.1829    0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9462   -1.8671   -1.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5688   -3.0664   -1.7746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6555   -4.1159   -2.2958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7921   -3.2303   -1.8459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195   -1.7227   -1.1305 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2965   -0.3127    0.2126 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1941    1.4757    0.5748 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2411    0.8799   -1.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7788    0.7094    2.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1579    0.5140   -0.9582 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6852    1.3523    0.3598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2970    1.2796    0.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7400   -1.3281   -0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4035    0.7460    0.1223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3916    2.9746    1.2146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2840    4.0587    1.7303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1654    2.8961    1.1448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3025   -3.8439   -3.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7515   -4.1496   -1.6503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1546   -5.1028   -2.3810 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
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 20  2  0
 20 19  1  0
 19 18  2  0
 18 17  1  0
 17 16  2  0
 13 21  1  0
 21 25  2  0
 21 22  1  0
 22 23  1  0
 22 24  2  0
 25 10  1  0
 20 12  1  0
 16 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  5 29  1  0
  6 30  1  0
  7 31  1  0
 11 32  1  0
 14 33  1  0
 19 37  1  0
 18 36  1  0
 17 35  1  0
 16 34  1  0
 23 38  1  0
 23 39  1  0
 23 40  1  0
M  END


  Mrv1652309062222562D          

 25 27  0  0  0  0            999 V2000
    8.3345    2.9634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7825    2.3503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9755    2.5218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7206    3.3064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4235    1.9087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6165    2.0803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0645    1.4672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    1.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0025    2.4233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703   -1.3283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1113   -1.7698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 N   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  2  0  0  0  0
  3  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
  8 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
 13 14  1  0  0  0  0
 14 15  1  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
 19 20  1  0  0  0  0
 15 20  2  0  0  0  0
 12 20  1  0  0  0  0
 13 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 21 25  2  0  0  0  0
 10 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0237707

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)\C=C\NC(=O)C1=CC2=C(NC3=C2C=CC=C3)C(=N1)C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H15N3O4/c1-10(22)16-17-12(11-5-3-4-6-13(11)20-17)9-14(21-16)18(24)19-8-7-15(23)25-2/h3-9,20H,1-2H3,(H,19,24)/b8-7+

> <INCHI_KEY>
UJECFLWSXCNVMR-BQYQJAHWSA-N

> <FORMULA>
C18H15N3O4

> <MOLECULAR_WEIGHT>
337.335

> <EXACT_MASS>
337.106255975

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
35.5786479797101

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2E)-3-({1-acetyl-9H-pyrido[3,4-b]indol-3-yl}formamido)prop-2-enoate

> <JCHEM_LOGP>
1.586917957666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.335685723696653

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.137068593688529

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1818210992239795

> <JCHEM_POLAR_SURFACE_AREA>
101.14999999999999

> <JCHEM_REFRACTIVITY>
90.7261

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2E)-3-({1-acetyl-9H-pyrido[3,4-b]indol-3-yl}formamido)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      15.558   5.532   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      14.527   4.387   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      13.021   4.707   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      12.545   6.172   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      11.990   3.563   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.484   3.883   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       9.454   2.739   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       7.947   3.059   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.471   4.524   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.838  -2.159   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.344  -2.479   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.808  -3.304   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       7.393   0.450   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   25                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   20                                                  
CONECT   13   12   14   21                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   12                                                  
CONECT   21   13   22   25                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   21   10                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

View in JSmol

Synonyms

Value	Source
Methyl(e)-3-[(1-acetyl-9H-pyrido[3,4-b]indole-3-carbonyl)amino]prop-2-enoate	ChEBI
Methyl(e)-3-[(1-acetyl-9H-pyrido[3,4-b]indole-3-carbonyl)amino]prop-2-enoic acid	Generator

Chemical Formula

C₁₈H₁₅N₃O₄

Average Mass

337.3350 Da

Monoisotopic Mass

337.10626 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC(=O)\C=C\NC(=O)C1=CC2=C(NC3=C2C=CC=C3)C(=N1)C(C)=O

InChI Identifier

InChI=1S/C18H15N3O4/c1-10(22)16-17-12(11-5-3-4-6-13(11)20-17)9-14(21-16)18(24)19-8-7-15(23)25-2/h3-9,20H,1-2H3,(H,19,24)/b8-7+

InChI Key

UJECFLWSXCNVMR-BQYQJAHWSA-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
Stellaria dichotoma	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
Pyridoindole
Indole
Indole or derivatives
Pyridine carboxylic acid or derivatives
2-heteroaryl carboxamide
Aryl ketone
Aryl alkyl ketone
Benzenoid
Pyridine
Heteroaromatic compound
Acrylic acid or derivatives
Pyrrole
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Vinylogous amide
Methyl ester
Carboxamide group
Carboxylic acid ester
Ketone
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid amide (CHEBI:70211 )
organic heterotricyclic compound (CHEBI:70211 )
methyl ester (CHEBI:70211 )
aromatic ketone (CHEBI:70211 )
beta-carboline alkaloid (CHEBI:70211 )

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

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

26389719

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

50906291

PDB ID

Not Available

ChEBI ID

70211

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for dichotomide iii (NP0237707)

MOL for NP0237707 (dichotomide iii)

3D MOL for NP0237707 (dichotomide iii)

3D SDF for NP0237707 (dichotomide iii)

3D-SDF for NP0237707 (dichotomide iii)

PDB for NP0237707 (dichotomide iii)

3D PDB for NP0237707 (dichotomide iii)

SMILES for NP0237707 (dichotomide iii)

INCHI for NP0237707 (dichotomide iii)

Structure for NP0237707 (dichotomide iii)

3D Structure for NP0237707 (dichotomide iii)