NP-MRD: Showing NP-Card for Hodgkinsine (NP0050876)

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Record Information

Version

2.0

Created at

2022-04-27 22:19:52 UTC

Updated at

2022-04-27 22:19:52 UTC

NP-MRD ID

NP0050876

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hodgkinsine

Description

Hodgkinsine 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 is found in Hodgkinsonia frutescens, Psychotria colorata, Psychotria lyciiflora, Psychotria malayana and Psychotria oleoides. Hodgkinsine was first documented in 2007 (PMID: 17887704). Based on a literature review a small amount of articles have been published on Hodgkinsine (PMID: 29168485) (PMID: 29058431) (PMID: 23203932) (PMID: 21919143).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200192D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282200192D          

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    1.2510   -0.7535    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5933   -1.2515    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2316   -1.2677    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710   -2.0572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059   -2.5289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -0.5568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7313   -1.0377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2953   -1.6398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0559   -2.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2525   -2.6167    0.0000 C   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
  3  4  1  0  0  0  0
  5  4  1  6  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  6  9  1  0  0  0  0
  3 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
  2 13  1  0  0  0  0
  1 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
 18 17  1  1  0  0  0
 14 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 14 21  1  0  0  0  0
 19 22  1  0  0  0  0
 16 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 15 26  1  0  0  0  0
 27 23  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 31 30  1  1  0  0  0
 27 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 27 34  1  0  0  0  0
 32 35  1  0  0  0  0
 29 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 28 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050876

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CC[C@]2([C@@H]1NC1=C2C=CC=C1)C1=CC=CC2=C1N[C@@H]1N(C)CC[C@]21[C@@]12CCN(C)[C@@H]1NC1=C2C=CC=C1

> <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-BDMNMGLZSA-N

> <FORMULA>
C33H38N6

> <MOLECULAR_WEIGHT>
518.709

> <EXACT_MASS>
518.315795248

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
57.40014818253963

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3aR,8aR)-7-[(3aR,8aR)-1-methyl-1H,2H,3H,3aH,8H,8aH-pyrrolo[2,3-b]indol-3a-yl]-3a-[(3aS,8aS)-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>
14.690206395211678

> <JCHEM_PKA_STRONGEST_BASIC>
7.6076969194614055

> <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>
hodgkinsine

> <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       1.649  -9.676   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.422 -10.605   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.926 -12.060   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.466 -12.030   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.913 -10.556   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.141  -9.626   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.821  -8.286   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.096  -8.202   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.563 -10.218   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.081 -13.225   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.594 -12.934   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.098 -11.479   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.906 -10.430   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.386  -8.795   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.614  -7.865   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.109  -6.411   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -0.431  -6.441   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -0.878  -7.915   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -2.105  -8.844   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -1.601 -10.299   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.061 -10.269   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.655  -8.205   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.117  -5.246   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.629  -5.536   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.134  -6.991   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.126  -8.156   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.612  -3.791   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.152  -3.761   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.599  -2.287   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       2.335  -1.406   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       1.107  -2.336   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      -0.432  -2.366   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      -0.879  -3.840   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.384  -4.721   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.400  -1.039   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.098  -1.937   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.151  -3.061   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.704  -4.535   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       4.205  -4.885   0.000  0.00  0.00           C+0
CONECT    1    2    5    8   14                                             
CONECT    2    1    3   13                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    1                                                       
CONECT    9    6                                                            
CONECT   10    3   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    2                                                       
CONECT   14    1   15   18   21                                             
CONECT   15   14   16   26                                                  
CONECT   16   15   17   23                                                  
CONECT   17   16   18                                                       
CONECT   18   17   14   19                                                  
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20   14                                                       
CONECT   22   19                                                            
CONECT   23   16   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   15                                                       
CONECT   27   23   28   31   34                                             
CONECT   28   27   29   39                                                  
CONECT   29   28   30   36                                                  
CONECT   30   29   31                                                       
CONECT   31   30   27   32                                                  
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33   27                                                       
CONECT   35   32                                                            
CONECT   36   29   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   28                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   94    0
END

View in JSmol

Synonyms

Value	Source
Hodgkinsine b	MeSH

Chemical Formula

C₃₃H₃₈N₆

Average Mass

518.7090 Da

Monoisotopic Mass

518.31580 Da

IUPAC Name

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

hodgkinsine

CAS Registry Number

Not Available

SMILES

CN1CC[C@]2([C@@H]1NC1=C2C=CC=C1)C1=CC=CC2=C1N[C@@H]1N(C)CC[C@]21[C@@]12CCN(C)[C@@H]1NC1=C2C=CC=C1

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-BDMNMGLZSA-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
Hodgkinsonia frutescens	Plant	KNApSAcK
Psychotria colorata	Plant	KNApSAcK
Psychotria lyciiflora	Plant	KNApSAcK
Psychotria malayana	Plant	KNApSAcK
Psychotria oleoides	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
Indole
Dihydroindole
Secondary aliphatic/aromatic amine
Benzenoid
N-alkylpyrrolidine
Pyrrole
Pyrrolidine
Azacycle
Secondary amine
Hydrocarbon derivative
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

pyrroloindole (CHEBI:5741 )
Indole alkaloids (C09211 )

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	57.4 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

C00001738

Chemspider ID

390632

KEGG Compound ID

C09211

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Hodgkinsine

METLIN ID

Not Available

PubChem Compound

442105

PDB ID

Not Available

ChEBI ID

5741

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 (NP0050876)

MOL for NP0050876 (Hodgkinsine)

3D MOL for NP0050876 (Hodgkinsine)

3D SDF for NP0050876 (Hodgkinsine)

3D-SDF for NP0050876 (Hodgkinsine)

PDB for NP0050876 (Hodgkinsine)

3D PDB for NP0050876 (Hodgkinsine)

SMILES for NP0050876 (Hodgkinsine)

INCHI for NP0050876 (Hodgkinsine)

Structure for NP0050876 (Hodgkinsine)

3D Structure for NP0050876 (Hodgkinsine)