NP-MRD: Showing NP-Card for (R)-(-)-Dichotomine C (NP0068655)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-28 13:54:49 UTC

Updated at

2022-04-28 13:54:49 UTC

NP-MRD ID

NP0068655

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(R)-(-)-Dichotomine C

Description

Dichotomine C 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. (R)-(-)-Dichotomine C is found in Stellaria dichotoma. (R)-(-)-Dichotomine C was first documented in 2008 (PMID: 18239319). Based on a literature review very few articles have been published on dichotomine C.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 37  0  0  0  0  0  0  0  0999 V2000
    1.4338    4.7401    2.1891 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2567    3.4546    1.6254 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0612    3.0197    1.1040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9225    3.7856    1.1151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0856    1.6686    0.5318 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9759    0.7760    0.4948 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8576   -0.4915   -0.0285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3754   -0.8996   -0.5435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2633   -2.1796   -0.9959 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9912   -2.6327   -0.8009 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5980   -3.8395   -1.0725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9130   -3.9697   -0.7312 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6395   -2.9543   -0.1359 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0011   -1.7594    0.1229 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6801   -1.5810   -0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4033   -0.0126   -0.4994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7027   -0.3624   -1.0507 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1518   -1.6351   -0.9012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7993    0.5939   -0.6016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3811    1.9057   -0.7023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2462    1.2179    0.0212 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8576    4.6978    3.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0537    5.5516    1.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5269    4.8595    2.4139 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9232    1.1039    0.8944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0461   -2.7177   -1.4300 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0244   -4.6265   -1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4161   -4.9051   -0.9332 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6757   -3.1146    0.1090 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5538   -0.9542    0.5886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6259   -0.1728   -2.1758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1316   -1.7368   -0.9096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1313    0.3500    0.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6865    0.4470   -1.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4868    2.3731    0.1885 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  2  0
  8  9  1  0
  9 10  1  0
 10 15  2  0
 15 14  1  0
 14 13  2  0
 13 12  1  0
 12 11  2  0
  8 16  1  0
 16 21  2  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 21  5  1  0
 15  7  1  0
 11 10  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  6 25  1  0
  9 26  1  0
 14 30  1  0
 13 29  1  0
 12 28  1  0
 11 27  1  0
 17 31  1  6
 18 32  1  0
 19 33  1  0
 19 34  1  0
 20 35  1  0
M  END


  Mrv1652304282215542D          

 21 23  0  0  1  0            999 V2000
    2.6014   -0.2006    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
    1.5214    0.5840    0.0000 C   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
    1.9339   -0.6855    0.0000 N   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 N   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
   -0.3896    1.6387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1347    2.4233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1966    1.4672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7486    2.0803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2046   -1.1567    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7566   -1.7698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5017   -2.5545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6024   -1.3283    0.0000 O   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
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  6 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  6  0  0  0
  2 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
  1 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068655

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CC2=C(NC3=C2C=CC=C3)C(=N1)[C@@H](O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C15H14N2O4/c1-21-15(20)11-6-9-8-4-2-3-5-10(8)16-13(9)14(17-11)12(19)7-18/h2-6,12,16,18-19H,7H2,1H3/t12-/m0/s1

> <INCHI_KEY>
WKUVQUIYZHZZFT-LBPRGKRZSA-N

> <FORMULA>
C15H14N2O4

> <MOLECULAR_WEIGHT>
286.287

> <EXACT_MASS>
286.095356939

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
29.91784289018642

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 1-[(1R)-1,2-dihydroxyethyl]-9H-pyrido[3,4-b]indole-3-carboxylate

> <ALOGPS_LOGP>
1.21

> <JCHEM_LOGP>
0.8985169506666666

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.281945097075518

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.575109935462947

> <JCHEM_PKA_STRONGEST_BASIC>
1.6149601643829803

> <JCHEM_POLAR_SURFACE_AREA>
95.44000000000001

> <JCHEM_REFRACTIVITY>
75.29990000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 1-[(1R)-1,2-dihydroxyethyl]-9H-pyrido[3,4-b]indole-3-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.173   0.450   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.727   3.059   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.251   4.524   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.234   2.739   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -3.264   3.883   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.382  -2.159   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.412  -3.304   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.936  -4.768   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.124  -2.479   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.393   0.450   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
CONECT    1    2    5   21                                                  
CONECT    2    1    3   18                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
CONECT   14    6   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14                                                            
CONECT   18    2   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    1                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
(S)-(-)-Dichotomine C	MeSH

Chemical Formula

C₁₅H₁₄N₂O₄

Average Mass

286.2870 Da

Monoisotopic Mass

286.09536 Da

IUPAC Name

methyl 1-[(1R)-1,2-dihydroxyethyl]-9H-pyrido[3,4-b]indole-3-carboxylate

Traditional Name

methyl 1-[(1R)-1,2-dihydroxyethyl]-9H-pyrido[3,4-b]indole-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CC2=C(NC3=C2C=CC=C3)C(=N1)[C@@H](O)CO

InChI Identifier

InChI=1S/C15H14N2O4/c1-21-15(20)11-6-9-8-4-2-3-5-10(8)16-13(9)14(17-11)12(19)7-18/h2-6,12,16,18-19H,7H2,1H3/t12-/m0/s1

InChI Key

WKUVQUIYZHZZFT-LBPRGKRZSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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	Plant	KNApSAcK

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
Pyridine carboxylic acid or derivatives
Pyridine
Benzenoid
Methyl ester
Pyrrole
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
1,2-diol
Carboxylic acid derivative
Organoheterocyclic compound
Azacycle
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aromatic alcohol
Alcohol
Organic nitrogen compound
Organooxygen compound
Primary alcohol
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	1.21	ALOGPS
logP	0.9	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	11.58	ChemAxon
pKa (Strongest Basic)	1.61	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	95.44 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	75.3 m³·mol⁻¹	ChemAxon
Polarizability	29.92 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

C00026654

Chemspider ID

9429700

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11254673

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Omura K, Choshi T, Watanabe S, Satoh Y, Nobuhiro J, Hibino S: The enantioselective total synthesis of a beta-carboline alkaloid, (S)-(-)-dichotomine C. Chem Pharm Bull (Tokyo). 2008 Feb;56(2):237-8. doi: 10.1248/cpb.56.237. [PubMed:18239319 ]

Showing NP-Card for (R)-(-)-Dichotomine C (NP0068655)

MOL for NP0068655 ((R)-(-)-Dichotomine C)

3D MOL for NP0068655 ((R)-(-)-Dichotomine C)

3D SDF for NP0068655 ((R)-(-)-Dichotomine C)

3D-SDF for NP0068655 ((R)-(-)-Dichotomine C)

PDB for NP0068655 ((R)-(-)-Dichotomine C)

3D PDB for NP0068655 ((R)-(-)-Dichotomine C)

SMILES for NP0068655 ((R)-(-)-Dichotomine C)

INCHI for NP0068655 ((R)-(-)-Dichotomine C)

Structure for NP0068655 ((R)-(-)-Dichotomine C)

3D Structure for NP0068655 ((R)-(-)-Dichotomine C)