NP-MRD: Showing NP-Card for (-)-Hodgkinsine B (NP0068715)

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Record Information

Version

2.0

Created at

2022-04-28 13:58:37 UTC

Updated at

2022-04-28 13:58:37 UTC

NP-MRD ID

NP0068715

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Hodgkinsine B

Description

Hodgkinsine B belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. (-)-Hodgkinsine B is found in Psychotria sp. (-)-Hodgkinsine B was first documented in 2007 (PMID: 17887704). Based on a literature review a small amount of articles have been published on hodgkinsine B (PMID: 29168485) (PMID: 29058431) (PMID: 23203932) (PMID: 21919143).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282215582D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282215582D          

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    4.3402   -2.0146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7762   -2.6167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9727   -2.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2959   -2.9010    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6381   -2.4030    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8133   -2.3868    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5739   -1.5973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2507   -1.1256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3032   -3.1079    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
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
  9 14  1  1  0  0  0
 14 15  1  1  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  1  0  0  0
 14 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 14 25  1  0  0  0  0
 23 26  1  0  0  0  0
 27 19  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 28 33  1  0  0  0  0
 33 34  1  0  0  0  0
 35 34  1  6  0  0  0
 27 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 27 38  1  0  0  0  0
 36 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068715

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CC[C@]2([C@@H]1NC1=CC=CC=C21)C1=C2N[C@H]3N(C)CC[C@]3(C2=CC=C1)[C@]12CCN(C)[C@H]1NC1=CC=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C33H38N6/c1-37-18-15-31(21-9-4-6-13-25(21)34-28(31)37)23-11-8-12-24-27(23)36-30-33(24,17-20-39(30)3)32-16-19-38(2)29(32)35-26-14-7-5-10-22(26)32/h4-14,28-30,34-36H,15-20H2,1-3H3/t28-,29-,30+,31-,32+,33-/m1/s1

> <INCHI_KEY>
DPVWJPVYOXKFRQ-BFZJMCNQSA-N

> <FORMULA>
C33H38N6

> <MOLECULAR_WEIGHT>
518.709

> <EXACT_MASS>
518.315795248

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
57.61396247949447

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3aS,8aS)-3a,7-bis[(3aR,8aR)-1-methyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-3a-yl]-1-methyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indole

> <ALOGPS_LOGP>
4.38

> <JCHEM_LOGP>
4.107322431

> <ALOGPS_LOGS>
-4.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.41838147043067

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.69020639521168

> <JCHEM_PKA_STRONGEST_BASIC>
7.607696919461405

> <JCHEM_POLAR_SURFACE_AREA>
45.81

> <JCHEM_REFRACTIVITY>
171.89579999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.96e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3aS,8aS)-3a,7-bis[(3aR,8aR)-1-methyl-2H,3H,8H,8aH-pyrrolo[2,3-b]indol-3a-yl]-1-methyl-2H,3H,8H,8aH-pyrrolo[2,3-b]indole

> <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       0.357   6.112   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.148   4.657   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.045   3.608   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.372   3.783   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.877   5.238   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.869   6.403   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.416   5.208   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       4.863   3.734   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.600   2.854   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.047   1.380   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.771   1.465   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       6.091   2.805   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       7.565   3.252   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.336   1.973   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.564   1.044   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.076   1.334   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.084   0.170   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.580  -1.285   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.067  -1.576   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.059  -0.411   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       1.520  -0.381   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       1.073   1.093   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      -0.155   2.022   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       0.350   3.477   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.889   3.447   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.714   1.393   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.562  -3.031   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.102  -3.061   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.155  -1.937   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.655  -2.287   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.102  -3.761   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.049  -4.885   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.549  -4.535   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       4.286  -5.415   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       3.058  -4.486   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       1.518  -4.455   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       1.071  -2.982   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.335  -2.101   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.566  -5.801   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                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8    4   10   14                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8   13                                                  
CONECT   13   12                                                            
CONECT   14    9   15   22   25                                             
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   27                                                  
CONECT   20   19   15   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   14   23                                                  
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   14                                                       
CONECT   26   23                                                            
CONECT   27   19   28   35   38                                             
CONECT   28   27   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   28   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   27   36                                                  
CONECT   36   35   37   39                                                  
CONECT   37   36   38                                                       
CONECT   38   37   27                                                       
CONECT   39   36                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   94    0
END

View in JSmol

Synonyms

Value	Source
Hodgkinsine	MeSH

Chemical Formula

C₃₃H₃₈N₆

Average Mass

518.7090 Da

Monoisotopic Mass

518.31580 Da

IUPAC Name

(3aS,8aS)-3a,7-bis[(3aR,8aR)-1-methyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-3a-yl]-1-methyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indole

Traditional Name

(3aS,8aS)-3a,7-bis[(3aR,8aR)-1-methyl-2H,3H,8H,8aH-pyrrolo[2,3-b]indol-3a-yl]-1-methyl-2H,3H,8H,8aH-pyrrolo[2,3-b]indole

CAS Registry Number

Not Available

SMILES

CN1CC[C@]2([C@@H]1NC1=CC=CC=C21)C1=C2N[C@H]3N(C)CC[C@]3(C2=CC=C1)[C@]12CCN(C)[C@H]1NC1=CC=CC=C21

InChI Identifier

InChI=1S/C33H38N6/c1-37-18-15-31(21-9-4-6-13-25(21)34-28(31)37)23-11-8-12-24-27(23)36-30-33(24,17-20-39(30)3)32-16-19-38(2)29(32)35-26-14-7-5-10-22(26)32/h4-14,28-30,34-36H,15-20H2,1-3H3/t28-,29-,30+,31-,32+,33-/m1/s1

InChI Key

DPVWJPVYOXKFRQ-BFZJMCNQSA-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
Psychotria sp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyrroloindoles

Direct Parent

Pyrroloindoles

Alternative Parents

Substituents

Pyrroloindole
Dihydroindole
Indole
Benzenoid
N-alkylpyrrolidine
Pyrrolidine
Pyrrole
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen 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	4.38	ALOGPS
logP	4.11	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	14.69	ChemAxon
pKa (Strongest Basic)	7.61	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	45.81 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	171.9 m³·mol⁻¹	ChemAxon
Polarizability	57.61 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00026751

Chemspider ID

30987742

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12041884

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jamison CR, Badillo JJ, Lipshultz JM, Comito RJ, MacMillan DWC: Catalyst-controlled oligomerization for the collective synthesis of polypyrroloindoline natural products. Nat Chem. 2017 Dec;9(12):1165-1169. doi: 10.1038/nchem.2825. Epub 2017 Jul 24. [PubMed:29168485 ]
Lindovska P, Movassaghi M: Concise Synthesis of (-)-Hodgkinsine, (-)-Calycosidine, (-)-Hodgkinsine B, (-)-Quadrigemine C, and (-)-Psycholeine via Convergent and Directed Modular Assembly of Cyclotryptamines. J Am Chem Soc. 2017 Dec 6;139(48):17590-17596. doi: 10.1021/jacs.7b09929. Epub 2017 Nov 20. [PubMed:29058431 ]
Snell RH, Durbin MJ, Woodward RL, Willis MC: Catalytic enantioselective desymmetrisation as a tool for the synthesis of hodgkinsine and hodgkinsine B. Chemistry. 2012 Dec 21;18(52):16754-64. doi: 10.1002/chem.201203150. Epub 2012 Nov 30. [PubMed:23203932 ]
Snell RH, Woodward RL, Willis MC: Catalytic enantioselective total synthesis of hodgkinsine B. Angew Chem Int Ed Engl. 2011 Sep 19;50(39):9116-9. doi: 10.1002/anie.201103864. Epub 2011 Aug 24. [PubMed:21919143 ]
Kodanko JJ, Hiebert S, Peterson EA, Sung L, Overman LE, de Moura Linck V, Goerck GC, Amador TA, Leal MB, Elisabetsky E: Synthesis of all low-energy stereoisomers of the tris(pyrrolidinoindoline) alkaloid hodgkinsine and preliminary assessment of their antinociceptive activity. J Org Chem. 2007 Oct 12;72(21):7909-14. doi: 10.1021/jo7013643. Epub 2007 Sep 21. [PubMed:17887704 ]

Showing NP-Card for (-)-Hodgkinsine B (NP0068715)

MOL for NP0068715 ((-)-Hodgkinsine B)

3D MOL for NP0068715 ((-)-Hodgkinsine B)

3D SDF for NP0068715 ((-)-Hodgkinsine B)

3D-SDF for NP0068715 ((-)-Hodgkinsine B)

PDB for NP0068715 ((-)-Hodgkinsine B)

3D PDB for NP0068715 ((-)-Hodgkinsine B)

SMILES for NP0068715 ((-)-Hodgkinsine B)

INCHI for NP0068715 ((-)-Hodgkinsine B)

Structure for NP0068715 ((-)-Hodgkinsine B)

3D Structure for NP0068715 ((-)-Hodgkinsine B)