NP-MRD: Showing NP-Card for Holantosine F (NP0067702)

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Record Information

Version

2.0

Created at

2022-04-28 12:32:34 UTC

Updated at

2022-04-28 12:32:34 UTC

NP-MRD ID

NP0067702

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Holantosine F

Description

(2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0¹,¹⁴.0²,¹¹.0⁵,¹⁰.0¹⁴,¹⁸]Henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. Holantosine F is found in Holarrhena antidysenterica . Based on a literature review very few articles have been published on (2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0¹,¹⁴.0²,¹¹.0⁵,¹⁰.0¹⁴,¹⁸]Henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282214322D          

 34 40  0  0  1  0            999 V2000
    0.3771   -1.0434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4848   -0.6798    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.1141   -0.3105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9329   -0.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4295   -0.8687    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.5637   -1.3263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8 13  1  0  0  0  0
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 15 20  1  0  0  0  0
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 23 24  1  0  0  0  0
  9 25  1  0  0  0  0
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  7 27  1  0  0  0  0
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 28  1  1  6  0  0  0
  4 28  1  0  0  0  0
 28 29  1  0  0  0  0
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  3 30  1  6  0  0  0
  8 31  1  1  0  0  0
  4 32  1  6  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
  2 34  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282214322D          

 34 40  0  0  1  0            999 V2000
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  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 11 14  1  6  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  1  0  0  0
 18 22  1  1  0  0  0
 17 23  1  1  0  0  0
 23 24  1  0  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  1  0  0  0
  7 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28  1  1  6  0  0  0
  4 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
  3 30  1  6  0  0  0
  8 31  1  1  0  0  0
  4 32  1  6  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
  2 34  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0067702

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1C[C@@H](O[C@H]2CC[C@]3(C)[C@@H](CC[C@@H]4[C@H]3CC[C@@]35CO[C@@]6(C)O[C@@]43CC[C@@H]56)C2)O[C@H](C)[C@@H]1N

> <INCHI_IDENTIFIER>
InChI=1S/C28H45NO5/c1-16-24(29)21(30-4)14-23(32-16)33-18-7-10-25(2)17(13-18)5-6-20-19(25)8-11-27-15-31-26(3)22(27)9-12-28(20,27)34-26/h16-24H,5-15,29H2,1-4H3/t16-,17+,18+,19-,20-,21-,22-,23-,24+,25-,26+,27+,28+/m1/s1

> <INCHI_KEY>
WBFUKUDNJLPCFA-GHRUGNLMSA-N

> <FORMULA>
C28H45NO5

> <MOLECULAR_WEIGHT>
475.67

> <EXACT_MASS>
475.329773553

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.50183535777269

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0^{1,14}.0^{2,11}.0^{5,10}.0^{14,18}]henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine

> <ALOGPS_LOGP>
3.54

> <JCHEM_LOGP>
3.8065972026666666

> <ALOGPS_LOGS>
-6.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.133377354178968

> <JCHEM_POLAR_SURFACE_AREA>
72.17

> <JCHEM_REFRACTIVITY>
127.5961

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0^{1,14}.0^{2,11}.0^{5,10}.0^{14,18}]henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine

> <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  O   UNK     0       0.704  -1.948   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.905  -1.269   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.022  -2.499   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.478  -1.997   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.080  -0.580   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.608  -0.392   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.535  -1.622   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.063  -1.434   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.990  -2.664   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.519  -2.476   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.120  -1.058   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.194   0.172   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.665  -0.016   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      10.649  -0.870   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      11.251   0.547   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.324   1.777   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.925   3.195   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.454   3.383   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.381   2.153   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.779   0.735   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      14.909   2.341   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      13.055   4.800   0.000  0.00  0.00           N+0
HETATM   23  O   UNK     0       9.998   4.425   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      10.600   5.842   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.389  -4.081   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.860  -4.269   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.933  -3.039   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.405  -3.227   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.522  -4.489   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.049  -4.038   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.137  -0.204   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.451  -0.457   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.022  -0.007   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.385  -1.695   0.000  0.00  0.00           C+0
CONECT    1    2   28                                                       
CONECT    2    1    3   33   34                                             
CONECT    3    2    4   30                                                  
CONECT    4    3    5   28   32                                             
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9   13   31                                             
CONECT    9    8   10   25                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19                                                            
CONECT   22   18                                                            
CONECT   23   17   24                                                       
CONECT   24   23                                                            
CONECT   25    9   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26    7   28                                                  
CONECT   28   27    1    4   29                                             
CONECT   29   28   30                                                       
CONECT   30   29    3                                                       
CONECT   31    8                                                            
CONECT   32    4   33                                                       
CONECT   33   32    2                                                       
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₅NO₅

Average Mass

475.6700 Da

Monoisotopic Mass

475.32977 Da

IUPAC Name

(2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0^{1,14}.0^{2,11}.0^{5,10}.0^{14,18}]henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine

Traditional Name

(2R,3S,4R,6S)-6-{[(1S,2R,5S,7S,10R,11R,14R,17S,18S)-10,17-dimethyl-16,21-dioxahexacyclo[15.3.1.0^{1,14}.0^{2,11}.0^{5,10}.0^{14,18}]henicosan-7-yl]oxy}-4-methoxy-2-methyloxan-3-amine

CAS Registry Number

Not Available

SMILES

CO[C@@H]1C[C@@H](O[C@H]2CC[C@]3(C)[C@@H](CC[C@@H]4[C@H]3CC[C@@]35CO[C@@]6(C)O[C@@]43CC[C@@H]56)C2)O[C@H](C)[C@@H]1N

InChI Identifier

InChI=1S/C28H45NO5/c1-16-24(29)21(30-4)14-23(32-16)33-18-7-10-25(2)17(13-18)5-6-20-19(25)8-11-27-15-31-26(3)22(27)9-12-28(20,27)34-26/h16-24H,5-15,29H2,1-4H3/t16-,17+,18+,19-,20-,21-,22-,23-,24+,25-,26+,27+,28+/m1/s1

InChI Key

WBFUKUDNJLPCFA-GHRUGNLMSA-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
Holarrhena pubescens	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
Naphthofuran
Furopyran
Ketal
Pyran
Oxane
Meta-dioxane
Tetrahydrofuran
Furan
Oxacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Acetal
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Primary aliphatic amine
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	3.54	ALOGPS
logP	3.81	ChemAxon
logS	-6.6	ALOGPS
pKa (Strongest Basic)	9.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.17 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	127.6 m³·mol⁻¹	ChemAxon
Polarizability	54.5 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

162853061

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Holantosine F (NP0067702)

MOL for NP0067702 (Holantosine F)

3D MOL for NP0067702 (Holantosine F)

3D SDF for NP0067702 (Holantosine F)

3D-SDF for NP0067702 (Holantosine F)

PDB for NP0067702 (Holantosine F)

3D PDB for NP0067702 (Holantosine F)

SMILES for NP0067702 (Holantosine F)

INCHI for NP0067702 (Holantosine F)

Structure for NP0067702 (Holantosine F)

3D Structure for NP0067702 (Holantosine F)