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Showing NP-Card for Calligonine (NP0050845)

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Record Information
Version2.0
Created at2022-04-27 22:15:11 UTC
Updated at2022-04-27 22:15:11 UTC
NP-MRD IDNP0050845
Secondary Accession NumbersNone
Natural Product Identification
Common NameCalligonine
DescriptionCalligonine, also known as elaeagnine or tetrahydroharman, 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. Calligonine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Calligonine is found in Banisteriopsis argentea, Calligonum minimum, Daphnia pulex, Elaeagnus angustifolia and Petalostylis labicheoides. Based on a literature review very few articles have been published on Calligonine.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0050845 (Calligonine)


  Mrv1652304282200152D          

 14 16  0  0  1  0            999 V2000
    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
    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
    2.8985    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
    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  2  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
    0.2046   -1.1567    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
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  8 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
  7 13  1  0  0  0  0
 10 14  1  1  0  0  0
M  END
Download

3D MOL for NP0050845 (Calligonine)

     RDKit          3D

 28 30  0  0  0  0  0  0  0  0999 V2000
   -2.5804    1.9272   -0.8157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0930    0.7201   -0.0860 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5551   -0.5276   -0.6493 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3333   -1.6045    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9252   -1.7096    0.7700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0800   -0.5732    0.3589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5895    0.6364   -0.0678 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4183    1.4511   -0.3659 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6066    0.8427   -0.1586 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9192    1.2378   -0.3096 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9482    0.3692   -0.0085 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6129   -0.8925    0.4434 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3165   -1.3038    0.6001 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3000   -0.4227    0.2944 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8816    2.7787   -0.7381 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8005    1.7428   -1.8868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5442    2.2551   -0.3559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3977    0.7613    0.9799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1134   -0.7109   -1.5815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0408   -1.4874    1.1169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6611   -2.5488   -0.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5212   -2.6901    0.4338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9314   -1.7041    1.8974 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3066    2.4429   -0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1541    2.2386   -0.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0054    0.6517   -0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4193   -1.5778    0.6811 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0415   -2.3027    0.9579 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
  7  2  1  0
 14  9  1  0
 14  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  1
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
M  END
Download

3D SDF for NP0050845 (Calligonine)


  Mrv1652304282200152D          

 14 16  0  0  1  0            999 V2000
    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
    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
    2.8985    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
    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  2  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
    0.2046   -1.1567    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
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  8 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
  7 13  1  0  0  0  0
 10 14  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0050845

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1NCCC2=C1NC1=CC=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C12H14N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-5,8,13-14H,6-7H2,1H3/t8-/m1/s1

> <INCHI_KEY>
LPIJOZBIVDCQTE-MRVPVSSYSA-N

> <FORMULA>
C12H14N2

> <MOLECULAR_WEIGHT>
186.258

> <EXACT_MASS>
186.115698459

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.637540826772174

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.30

> <JCHEM_LOGP>
2.0068212933333336

> <ALOGPS_LOGS>
-2.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.388921491986245

> <JCHEM_PKA_STRONGEST_BASIC>
9.158778232947299

> <JCHEM_POLAR_SURFACE_AREA>
27.82

> <JCHEM_REFRACTIVITY>
57.998400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
calligonine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0050845 (Calligonine)

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PDB for NP0050845 (Calligonine)
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       6.917   1.914   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.393   0.450   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -0.173   0.450   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.810   2.235   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
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    7                                                       
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

Download
3D PDB for NP0050845 (Calligonine)
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SMILES for NP0050845 (Calligonine)
C[C@H]1NCCC2=C1NC1=CC=CC=C21
Download
INCHI for NP0050845 (Calligonine)
InChI=1S/C12H14N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-5,8,13-14H,6-7H2,1H3/t8-/m1/s1
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View in JSmol
Synonyms
ValueSource
ElaeagnineKegg
TetrahydroharmanKegg
Chemical FormulaC12H14N2
Average Mass186.2580 Da
Monoisotopic Mass186.11570 Da
IUPAC Name(1R)-1-methyl-1H,2H,3H,4H,9H-pyrido[3,4-b]indole
Traditional Namecalligonine
CAS Registry NumberNot Available
SMILES
C[C@H]1NCCC2=C1NC1=CC=CC=C21
InChI Identifier
InChI=1S/C12H14N2/c1-8-12-10(6-7-13-8)9-4-2-3-5-11(9)14-12/h2-5,8,13-14H,6-7H2,1H3/t8-/m1/s1
InChI KeyLPIJOZBIVDCQTE-MRVPVSSYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Banisteriopsis argenteaPlant
Calligonum minimumPlant
Daphnia pulexLOTUS Database
Elaeagnus angustifoliaPlant
Petalostylis labicheoidesPlant
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.
KingdomOrganic compounds  
Super ClassAlkaloids and derivatives  
ClassHarmala alkaloids  
Sub ClassNot Available
Direct ParentHarmala alkaloids  
Alternative Parents
Substituents
  • Harman
    • 

  • Beta-carboline
    • 

  • Pyridoindole
    • 

  • 3-alkylindole
    • 

  • Indole
    • 

  • Indole or derivatives
    • 

  • Aralkylamine
    • 

  • Benzenoid
    • 

  • Heteroaromatic compound
    • 

  • Pyrrole
    • 

  • Secondary aliphatic amine
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Secondary amine
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.3ALOGPS
logP2.01ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)16.39ChemAxon
pKa (Strongest Basic)9.16ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area27.82 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity58 m³·mol⁻¹ChemAxon
Polarizability21.64 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00001699  
Chemspider ID390581  
KEGG Compound IDC09089  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTetrahydroharman  
METLIN IDNot Available
PubChem Compound442025  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available