NP-MRD: Showing NP-Card for dichotomide vi (NP0160396)

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Record Information

Version

2.0

Created at

2022-09-02 18:20:43 UTC

Updated at

2022-09-02 18:20:43 UTC

NP-MRD ID

NP0160396

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dichotomide vi

Description

Dichotomide VI 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 vi is found in Stellaria dichotoma. Dichotomide VI is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004251514142D          

 20 22  0  0  0  0            999 V2000
    1.2637   -4.1555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117   -3.5424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0953   -3.7139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9666   -2.7578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4146   -2.1447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6695   -1.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4765   -1.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0285   -1.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8535   -1.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4056   -1.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2125   -1.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4675   -2.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9154   -2.7578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1704   -3.5424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1085   -2.5862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4410   -3.0712    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7736   -2.5862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1175   -0.7470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6895   -0.9185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3724    0.0377    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  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  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
 13 15  1  0  0  0  0
  9 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  4 17  1  0  0  0  0
  8 17  2  0  0  0  0
  6 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0160396

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)C1=NC(=CC2=C1NC1=C2C=CC=C1O)C(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H11N3O3/c1-6(18)11-13-8(5-9(16-11)14(15)20)7-3-2-4-10(19)12(7)17-13/h2-5,17,19H,1H3,(H2,15,20)

> <INCHI_KEY>
BQCOVTPWSCEKDZ-UHFFFAOYSA-N

> <FORMULA>
C14H11N3O3

> <MOLECULAR_WEIGHT>
269.26

> <EXACT_MASS>
269.080041226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
27.280952860473025

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-acetyl-8-hydroxy-9H-pyrido[3,4-b]indole-3-carboxamide

> <ALOGPS_LOGP>
1.48

> <JCHEM_LOGP>
0.749636405

> <ALOGPS_LOGS>
-2.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.933090538814062

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.38093595997628

> <JCHEM_PKA_STRONGEST_BASIC>
0.019960105591409594

> <JCHEM_POLAR_SURFACE_AREA>
109.06999999999998

> <JCHEM_REFRACTIVITY>
72.03339999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.96e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-acetyl-8-hydroxy-9H-pyrido[3,4-b]indole-3-carboxamide

> <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       2.359  -7.757   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.328  -6.612   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.178  -6.933   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.804  -5.148   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.774  -4.003   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.250  -2.539   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.756  -2.219   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.787  -3.363   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.327  -3.363   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.357  -2.219   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.863  -2.539   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.339  -4.003   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.309  -5.148   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.785  -6.612   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.802  -4.828   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       4.557  -5.733   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       3.311  -4.828   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.219  -1.394   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.287  -1.715   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0       0.695   0.070   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   18                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    9   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16    4    8                                                  
CONECT   18    6   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₁N₃O₃

Average Mass

269.2600 Da

Monoisotopic Mass

269.08004 Da

IUPAC Name

1-acetyl-8-hydroxy-9H-pyrido[3,4-b]indole-3-carboxamide

Traditional Name

1-acetyl-8-hydroxy-9H-pyrido[3,4-b]indole-3-carboxamide

CAS Registry Number

Not Available

SMILES

CC(=O)C1=NC(=CC2=C1NC1=C2C=CC=C1O)C(N)=O

InChI Identifier

InChI=1S/C14H11N3O3/c1-6(18)11-13-8(5-9(16-11)14(15)20)7-3-2-4-10(19)12(7)17-13/h2-5,17,19H,1H3,(H2,15,20)

InChI Key

BQCOVTPWSCEKDZ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

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
Pyridoindole
Beta-carboline
Hydroxyindole
Pyridine carboxylic acid or derivatives
Indole or derivatives
Indole
2-heteroaryl carboxamide
Aryl alkyl ketone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyridine
Benzenoid
Pyrrole
Heteroaromatic compound
Vinylogous amide
Carboxamide group
Ketone
Primary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid amide (CHEBI:70214 )
phenols (CHEBI:70214 )
aromatic ketone (CHEBI:70214 )
beta-carboline alkaloid (CHEBI:70214 )

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	1.48	ALOGPS
logP	0.75	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.38	ChemAxon
pKa (Strongest Basic)	0.02	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	109.07 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	72.03 m³·mol⁻¹	ChemAxon
Polarizability	27.28 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

50906511

PDB ID

Not Available

ChEBI ID

70214

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for dichotomide vi (NP0160396)

MOL for NP0160396 (dichotomide vi)

3D MOL for NP0160396 (dichotomide vi)

3D SDF for NP0160396 (dichotomide vi)

3D-SDF for NP0160396 (dichotomide vi)

PDB for NP0160396 (dichotomide vi)

3D PDB for NP0160396 (dichotomide vi)

SMILES for NP0160396 (dichotomide vi)

INCHI for NP0160396 (dichotomide vi)

Structure for NP0160396 (dichotomide vi)

3D Structure for NP0160396 (dichotomide vi)