NP-MRD: Showing NP-Card for (11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine (NP0216418)

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Record Information

Version

2.0

Created at

2022-09-05 16:22:08 UTC

Updated at

2022-09-05 16:22:09 UTC

NP-MRD ID

NP0216418

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine

Description

Harmicine, also known as (R)-harmicine, belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. (11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine is found in Kopsia griffithii. (11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine was first documented in 2019 (PMID: 30895973). Based on a literature review a small amount of articles have been published on Harmicine (PMID: 34581483) (PMID: 34274829) (PMID: 32584573) (PMID: 32558575).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 35  0  0  0  0  0  0  0  0999 V2000
    4.4882    0.1888   -0.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1134   -0.9962    0.5844 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7803   -1.3518    0.6858 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8551   -0.4948    0.1628 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4901   -0.5868    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0260    0.5199   -0.5094 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0142    1.2852   -0.8508 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1664    0.6975   -0.4572 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5048    1.0258   -0.5436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4680    0.7235   -0.7162 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9892    1.8068    0.1859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2348    1.2430    0.8461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1853   -0.2151    0.5438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2679   -0.4226   -0.5483 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5791   -1.6704   -0.4422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4680   -1.6126    0.6070 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5429    0.4219   -0.0817 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8572   -1.6641    0.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -2.2699    1.1588 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0229    2.2131   -1.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7950    1.9462   -1.0189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6119    1.0998   -1.7711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2325    2.1294    0.9439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3033    2.7209   -0.3590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1962    1.3967    1.9469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1590    1.6688    0.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1736   -0.6363    0.2283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8616   -0.8199    1.4398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3071   -2.4295   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1707   -1.9778   -1.4100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8840   -1.3288    1.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0125   -2.6104    0.6223 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 10  1  0
 10 14  1  0
 14 13  1  0
 14 15  1  0
 15 16  1  0
 16  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
 13 12  1  0
  4  5  1  0
  6 10  1  0
  4  8  1  0
 12 25  1  0
 12 26  1  0
 11 23  1  0
 11 24  1  0
 10 22  1  6
 13 27  1  0
 13 28  1  0
 15 29  1  0
 15 30  1  0
 16 31  1  0
 16 32  1  0
  7 20  1  0
  9 21  1  0
  1 17  1  0
  2 18  1  0
  3 19  1  0
M  END


  Mrv1652309052218222D          

 16 19  0  0  1  0            999 V2000
    4.3123    1.1588    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    1.9819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173    2.3461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8317    1.8871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0319    2.0894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5924    1.3913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1205    0.7575    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8865    1.0639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6268    0.6998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7680    1.4229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1929    0.8314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5474    1.1956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4298    2.0122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3831    2.1527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8227    2.8508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6471    2.8192    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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
  6 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
 13 14  1  0  0  0  0
 10 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  5 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0216418

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C1C[C@@H]2N(C1)CCC1=C2NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C14H16N2/c1-2-5-12-10(4-1)11-7-9-16-8-3-6-13(16)14(11)15-12/h1-2,4-5,13,15H,3,6-9H2/t13-/m0/s1

> <INCHI_KEY>
LXJWBHIVLXMHDZ-ZDUSSCGKSA-N

> <FORMULA>
C14H16N2

> <MOLECULAR_WEIGHT>
212.296

> <EXACT_MASS>
212.131348523

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.9899350289152

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-6,16-diazatetracyclo[7.7.0.0^{2,6}.0^{10,15}]hexadeca-1(9),10,12,14-tetraene

> <JCHEM_LOGP>
2.438858742666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.375171237791147

> <JCHEM_PKA_STRONGEST_BASIC>
8.197818328514552

> <JCHEM_POLAR_SURFACE_AREA>
19.03

> <JCHEM_REFRACTIVITY>
66.08550000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-6,16-diazatetracyclo[7.7.0.0^{2,6}.0^{10,15}]hexadeca-1(9),10,12,14-tetraene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       8.050   2.163   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.947   3.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.566   4.379   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.286   3.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.793   3.900   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.972   2.597   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.958   1.414   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       5.388   1.986   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.770   1.306   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.434   2.656   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.360   1.552   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.022   2.232   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.802   3.756   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.715   4.018   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       1.536   5.321   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.075   5.262   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6   16                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8    1                                                       
CONECT   10    6   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15    5                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   38    0
END

View in JSmol

Synonyms

Value	Source
(R)-Harmicine	MeSH

Chemical Formula

C₁₄H₁₆N₂

Average Mass

212.2960 Da

Monoisotopic Mass

212.13135 Da

IUPAC Name

(2S)-6,16-diazatetracyclo[7.7.0.0^{2,6}.0^{10,15}]hexadeca-1(9),10,12,14-tetraene

Traditional Name

(2S)-6,16-diazatetracyclo[7.7.0.0^{2,6}.0^{10,15}]hexadeca-1(9),10,12,14-tetraene

CAS Registry Number

Not Available

SMILES

C1C[C@@H]2N(C1)CCC1=C2NC2=CC=CC=C12

InChI Identifier

InChI=1S/C14H16N2/c1-2-5-12-10(4-1)11-7-9-16-8-3-6-13(16)14(11)15-12/h1-2,4-5,13,15H,3,6-9H2/t13-/m0/s1

InChI Key

LXJWBHIVLXMHDZ-ZDUSSCGKSA-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
Kopsia griffithii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyridoindoles

Direct Parent

Beta carbolines

Alternative Parents

Substituents

Beta-carboline
3-alkylindole
Indole
Aralkylamine
Benzenoid
N-alkylpyrrolidine
Heteroaromatic compound
Pyrrole
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Azacycle
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Amine
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	2.44	ChemAxon
pKa (Strongest Acidic)	16.38	ChemAxon
pKa (Strongest Basic)	8.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	19.03 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	66.09 m³·mol⁻¹	ChemAxon
Polarizability	24.99 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

C00026538

Chemspider ID

9021517

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10846223

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liang L, Zhou S, Zhang W, Tong R: Catalytic Asymmetric Alkynylation of 3,4-Dihydro-beta-carbolinium Ions Enables Collective Total Syntheses of Indole Alkaloids. Angew Chem Int Ed Engl. 2021 Nov 15;60(47):25135-25142. doi: 10.1002/anie.202112383. Epub 2021 Oct 20. [PubMed:34581483 ]
Marinovic M, Poje G, Perkovic I, Fontinha D, Prudencio M, Held J, Pessanha de Carvalho L, Tandaric T, Vianello R, Rajic Z: Further investigation of harmicines as novel antiplasmodial agents: Synthesis, structure-activity relationship and insight into the mechanism of action. Eur J Med Chem. 2021 Nov 15;224:113687. doi: 10.1016/j.ejmech.2021.113687. Epub 2021 Jul 5. [PubMed:34274829 ]
Habel D, Nair DS, Kallingathodi Z, Mohan C, Pillai SM, Nair RR, Thomas G, Haleema S, Gopinath C, Abdul RV, Fritz M, Puente AR, Johnson JL, Polavarapu PL, Ibnusaud I: Natural Product-Derived Chiral Pyrrolidine-2,5-diones, Their Molecular Structures and Conversion to Pharmacologically Important Skeletons. J Nat Prod. 2020 Jul 24;83(7):2178-2190. doi: 10.1021/acs.jnatprod.0c00211. Epub 2020 Jun 25. [PubMed:32584573 ]
Nalikezhathu A, Cherepakhin V, Williams TJ: Ruthenium Catalyzed Tandem Pictet-Spengler Reaction. Org Lett. 2020 Jul 2;22(13):4979-4984. doi: 10.1021/acs.orglett.0c01485. Epub 2020 Jun 19. [PubMed:32558575 ]
Peczkowski GR, Craven PGE, Stead D, Simpkins NS: 2,7-Diazabicyclo[2.2.1]heptanes: novel asymmetric access and controlled bridge-opening. Chem Commun (Camb). 2019 Apr 4;55(29):4214-4217. doi: 10.1039/c8cc10263e. [PubMed:30895973 ]
LOTUS database [Link]

Showing NP-Card for (11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine (NP0216418)

MOL for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

3D MOL for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

3D SDF for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

3D-SDF for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

PDB for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

3D PDB for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

SMILES for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

INCHI for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

Structure for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)

3D Structure for NP0216418 ((11bs)-1h,2h,3h,5h,6h,11h,11bh-indolo[3,2-g]indolizine)