NP-MRD: Showing NP-Card for Polyneurine H (NP0332058)

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Record Information

Version

2.0

Created at

2023-10-31 20:06:10 UTC

Updated at

2024-09-03 04:17:50 UTC

NP-MRD ID

NP0332058

Natural Product DOI

https://doi.org/10.57994/1186

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Polyneurine H

Description

Polyneurine H belongs to the class of organic compounds known as ibogan-type alkaloids. These are indole alkaloids with a structure based on the ibogamine skeleton or a derivative thereof. Ibogamine is a pentacyclic heterocyclic compound consisting of an indole fused to an azepane-containing tricyclic moiety ring. Iboga alkaloids arise from the cyclization of a secodine-type precursor through the formation of a 16,21 bond. Polyneurine H was first documented in 2023 (PMID: 36646163). Based on a literature review very few articles have been published on Polyneurine H.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10312320062D          

 30 34  0  0  1  0            999 V2000
   -0.6427    0.9118    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1720    0.7820    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1299   -0.0603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9911   -0.1073    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4855   -0.7592    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2392   -0.8927    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2463   -1.8319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629   -0.6465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4337    0.7756    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2567    1.6451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3961    1.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8725    2.2598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6656    1.9656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9377    1.1693    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4292    1.9028    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5765    0.4275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1704   -0.1452    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8985    0.2426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6740   -0.0391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3056    0.4917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1618    1.3040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3864    1.5857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7548    1.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2158    1.0381    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764    0.0606    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7148   -0.9661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1944   -1.7329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8073   -2.4615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7770   -1.3088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9371    0.4623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  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
  2 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 14 23  1  0  0  0  0
  9 24  1  1  0  0  0
  9 25  1  0  0  0  0
 25 16  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 26 29  2  0  0  0  0
 25 30  1  0  0  0  0
  2 30  1  0  0  0  0
M  END


  Mrv2104 10312320062D          

 30 34  0  0  1  0            999 V2000
   -0.6427    0.9118    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1720    0.7820    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1299   -0.0603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9911   -0.1073    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4855   -0.7592    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2392   -0.8927    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2463   -1.8319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629   -0.6465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4337    0.7756    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2567    1.6451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3961    1.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8725    2.2598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6656    1.9656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9377    1.1693    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4292    1.9028    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5765    0.4275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1704   -0.1452    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8985    0.2426    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6740   -0.0391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3056    0.4917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1618    1.3040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3864    1.5857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7548    1.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2158    1.0381    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764    0.0606    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7148   -0.9661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1944   -1.7329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8073   -2.4615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7770   -1.3088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9371    0.4623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  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
  2 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 14 23  1  0  0  0  0
  9 24  1  1  0  0  0
  9 25  1  0  0  0  0
 25 16  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 26 29  2  0  0  0  0
 25 30  1  0  0  0  0
  2 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332058

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CN3CC[C@]4(O)C5=CC=CC=C5N=C4[C@@](C1)(C(=O)OC)[C@]3([H])[C@]([H])(C2)[C@@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C21H26N2O4/c1-12(24)14-9-13-10-20(19(25)27-2)17(14)23(11-13)8-7-21(26)15-5-3-4-6-16(15)22-18(20)21/h3-6,12-14,17,24,26H,7-11H2,1-2H3/t12-,13-,14-,17+,20+,21+/m1/s1

> <INCHI_KEY>
BPKMKKDJAWRIOB-LYZQFKNMSA-N

> <FORMULA>
C21H26N2O4

> <MOLECULAR_WEIGHT>
370.449

> <EXACT_MASS>
370.189257325

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
39.91315025457198

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1S,10S,15R,17S,18S)-10-hydroxy-17-[(1R)-1-hydroxyethyl]-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2,4,6,8-tetraene-1-carboxylate

> <JCHEM_LOGP>
1.6967025279999994

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.219011191307889

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.6822993830565

> <JCHEM_PKA_STRONGEST_BASIC>
8.609573330663704

> <JCHEM_POLAR_SURFACE_AREA>
82.36000000000001

> <JCHEM_REFRACTIVITY>
102.0947

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,10S,15R,17S,18S)-10-hydroxy-17-[(1R)-1-hydroxyethyl]-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2,4,6,8-tetraene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-OCT-23         0                                  
HETATM    1  H   UNK     0      -1.200   1.702   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       0.321   1.460   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.242  -0.113   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.850  -0.200   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0       0.906  -1.417   0.000  0.00  0.00           H+0
HETATM    6  C   UNK     0       2.313  -1.666   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.326  -3.420   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.037  -1.207   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.676   1.448   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.346   3.071   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       0.739   2.996   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.495   4.218   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.976   3.669   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.484   2.183   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.401   3.552   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.810   0.798   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       5.918  -0.271   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       7.277   0.453   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.725  -0.073   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.904   0.918   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.635   2.434   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.188   2.960   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.009   1.969   0.000  0.00  0.00           C+0
HETATM   24  H   UNK     0       4.136   1.938   0.000  0.00  0.00           H+0
HETATM   25  C   UNK     0       3.316   0.113   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.201  -1.803   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.096  -3.235   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.374  -4.595   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.450  -2.443   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.749   0.863   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11   30                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6    9                                             
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    4   10   24   25                                             
CONECT   10    9   11   12                                                  
CONECT   11   10    2                                                       
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   23                                             
CONECT   15   14                                                            
CONECT   16   14   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   18   14                                                  
CONECT   24    9                                                            
CONECT   25    9   16   26   30                                             
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26                                                            
CONECT   30   25    2                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₆N₂O₄

Average Mass

370.4490 Da

Monoisotopic Mass

370.18926 Da

IUPAC Name

methyl (1S,10S,15R,17S,18S)-10-hydroxy-17-[(1R)-1-hydroxyethyl]-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2,4,6,8-tetraene-1-carboxylate

Traditional Name

methyl (1S,10S,15R,17S,18S)-10-hydroxy-17-[(1R)-1-hydroxyethyl]-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2,4,6,8-tetraene-1-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@]12CN3CC[C@]4(O)C5=CC=CC=C5N=C4[C@@](C1)(C(=O)OC)[C@]3([H])[C@]([H])(C2)[C@@H](C)O

InChI Identifier

InChI=1S/C21H26N2O4/c1-12(24)14-9-13-10-20(19(25)27-2)17(14)23(11-13)8-7-21(26)15-5-3-4-6-16(15)22-18(20)21/h3-6,12-14,17,24,26H,7-11H2,1-2H3/t12-,13-,14-,17+,20+,21+/m1/s1

InChI Key

BPKMKKDJAWRIOB-LYZQFKNMSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2024-05-11	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
polyneura		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as ibogan-type alkaloids. These are indole alkaloids with a structure based on the ibogamine skeleton or a derivative thereof. Ibogamine is a pentacyclic heterocyclic compound consisting of an indole fused to an azepane-containing tricyclic moiety ring. Iboga alkaloids arise from the cyclization of a secodine-type precursor through the formation of a 16,21 bond.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Ibogan-type alkaloids

Sub Class

Not Available

Direct Parent

Ibogan-type alkaloids

Alternative Parents

Substituents

Ibogan skeleton
Catharanthine skeleton
3-alkylindole
Piperidinecarboxylic acid
Indole or derivatives
Fatty acid ester
Azepane
Fatty acyl
Benzenoid
Piperidine
Methyl ester
Tertiary alcohol
Secondary ketimine
Pyrroline
1,3-aminoalcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Ketimine
Carboxylic acid ester
Amino acid or derivatives
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Imine
Amine
Alcohol
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	1.7	ChemAxon
pKa (Strongest Acidic)	12.68	ChemAxon
pKa (Strongest Basic)	8.61	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	82.36 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	102.09 m³·mol⁻¹	ChemAxon
Polarizability	39.91 Å³	ChemAxon
Number of Rings	5	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tang SY, Tan CH, Sim KS, Yong KT, Lim KH, Low YY, Lim SH: Polyneurines A-H, iboga alkaloids from Tabernaemontana polyneura. Phytochemistry. 2023 Apr;208:113587. doi: 10.1016/j.phytochem.2023.113587. Epub 2023 Jan 14. [PubMed:36646163 ]

Showing NP-Card for Polyneurine H (NP0332058)

MOL for NP0332058 (Polyneurine H)

3D MOL for NP0332058 (Polyneurine H)

3D SDF for NP0332058 (Polyneurine H)

3D-SDF for NP0332058 (Polyneurine H)

PDB for NP0332058 (Polyneurine H)

3D PDB for NP0332058 (Polyneurine H)

SMILES for NP0332058 (Polyneurine H)

INCHI for NP0332058 (Polyneurine H)

Structure for NP0332058 (Polyneurine H)

3D Structure for NP0332058 (Polyneurine H)