NP-MRD: Showing NP-Card for (1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol (NP0243384)

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Record Information

Version

1.0

Created at

2022-09-07 03:55:18 UTC

Updated at

2022-09-07 03:55:18 UTC

NP-MRD ID

NP0243384

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol

Description

Persicanidine B belongs to the class of organic compounds known as cerveratrum-type alkaloids. These are steroidal alkaloids containing the cevane (23-methyl-4- azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]Pentacosane) moiety, which is a six ring system. Cerveratrum alkaloids have 7-9 oxygen atoms and occur as free alkamines or esters of simple aliphatic or aromatic acids. (1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol is found in Fritillaria persica. It was first documented in 2004 (PMID: 15143828). Based on a literature review a significant number of articles have been published on Persicanidine B (PMID: 36088123) (PMID: 36088122) (PMID: 36088121) (PMID: 36088120).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072205552D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309072205552D          

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 30 29  1  1  0  0  0
 15 30  1  0  0  0  0
 11 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0243384

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@H]2C(C)[C@@H]3CC[C@@H]4[C@@H](C[C@H]5[C@H]4C[C@@H](O)[C@H]4C[C@@H](O)CC[C@]54C)[C@@H]3CN2C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H45NO2/c1-15-4-7-25-16(2)18-5-6-19-20(22(18)14-28(25)13-15)11-23-21(19)12-26(30)24-10-17(29)8-9-27(23,24)3/h15-26,29-30H,4-14H2,1-3H3/t15-,16?,17+,18+,19-,20-,21+,22-,23+,24-,25+,26-,27-/m1/s1

> <INCHI_KEY>
NEMWYOKGHGSVSC-YMQQRAHFSA-N

> <FORMULA>
C27H45NO2

> <MOLECULAR_WEIGHT>
415.662

> <EXACT_MASS>
415.345029693

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
51.44238950261588

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,6R,9S,11R,14S,15S,17R,18S,20S,23R,24S)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]pentacosane-17,20-diol

> <JCHEM_LOGP>
3.9163617926666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.42014423408202

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.751598110791935

> <JCHEM_PKA_STRONGEST_BASIC>
8.947855081776618

> <JCHEM_POLAR_SURFACE_AREA>
43.7

> <JCHEM_REFRACTIVITY>
121.9326

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,6R,9S,11R,14S,15S,17R,18S,20S,23R,24S)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]pentacosane-17,20-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      11.379  -3.259   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.554  -1.958   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.269  -0.594   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.808  -0.531   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.522   0.833   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.698   2.134   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.413   3.498   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.160   2.071   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      10.445   0.707   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       8.906   0.644   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.192  -0.721   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.016  -2.022   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.301  -3.386   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.762  -3.449   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.938  -2.148   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.420  -1.890   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.212  -2.845   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.781  -2.277   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.573  -3.233   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.557  -0.754   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.126  -0.186   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.098   1.338   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.529   1.906   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.110   2.294   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.541   1.726   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.765   0.202   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.973   1.157   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.196  -0.366   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.576   0.317   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.653  -0.784   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    3   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   30                                                  
CONECT   12   11    2   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   30                                                  
CONECT   16   15   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   20   27   28                                             
CONECT   27   26                                                            
CONECT   28   26   16   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   15   11                                                  
MASTER        0    0    0    0    0    0    0    0   30    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₅NO₂

Average Mass

415.6620 Da

Monoisotopic Mass

415.34503 Da

IUPAC Name

(1R,2S,6R,9S,11R,14S,15S,17R,18S,20S,23R,24S)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]pentacosane-17,20-diol

Traditional Name

(1R,2S,6R,9S,11R,14S,15S,17R,18S,20S,23R,24S)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]pentacosane-17,20-diol

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@H]2C(C)[C@@H]3CC[C@@H]4[C@@H](C[C@H]5[C@H]4C[C@@H](O)[C@H]4C[C@@H](O)CC[C@]54C)[C@@H]3CN2C1

InChI Identifier

InChI=1S/C27H45NO2/c1-15-4-7-25-16(2)18-5-6-19-20(22(18)14-28(25)13-15)11-23-21(19)12-26(30)24-10-17(29)8-9-27(23,24)3/h15-26,29-30H,4-14H2,1-3H3/t15-,16?,17+,18+,19-,20-,21+,22-,23+,24-,25+,26-,27-/m1/s1

InChI Key

NEMWYOKGHGSVSC-YMQQRAHFSA-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
Fritillaria persica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cerveratrum-type alkaloids. These are steroidal alkaloids containing the cevane (23-methyl-4- azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]Pentacosane) moiety, which is a six ring system. Cerveratrum alkaloids have 7-9 oxygen atoms and occur as free alkamines or esters of simple aliphatic or aromatic acids.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Cerveratrum-type alkaloids

Alternative Parents

Substituents

Cerveratrum-type alkaloid
Azasteroid
Quinolizidine
Alkaloid or derivatives
Piperidine
Cyclic alcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
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	3.92	ChemAxon
pKa (Strongest Acidic)	14.75	ChemAxon
pKa (Strongest Basic)	8.95	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	43.7 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	121.93 m³·mol⁻¹	ChemAxon
Polarizability	51.44 Å³	ChemAxon
Number of Rings	6	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

C00028817

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

101635476

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xu X, Rothrock MJ Jr, Reeves J, Kumar GD, Mishra A: Using E. coli population to predict foodborne pathogens in pastured poultry farms. Food Microbiol. 2022 Dec;108:104092. doi: 10.1016/j.fm.2022.104092. Epub 2022 Jul 14. [PubMed:36088123 ]
Lanzl MI, Zwietering MH, Abee T, den Besten HMW: Combining enrichment with multiplex real-time PCR leads to faster detection and identification of Campylobacter spp. in food compared to ISO 10272-1:2017. Food Microbiol. 2022 Dec;108:104117. doi: 10.1016/j.fm.2022.104117. Epub 2022 Aug 19. [PubMed:36088122 ]
Cacciatore FA, Maders C, Alexandre B, Barreto Pinilla CM, Brandelli A, da Silva Malheiros P: Carvacrol encapsulation into nanoparticles produced from chia and flaxseed mucilage: Characterization, stability and antimicrobial activity against Salmonella and Listeria monocytogenes. Food Microbiol. 2022 Dec;108:104116. doi: 10.1016/j.fm.2022.104116. Epub 2022 Aug 18. [PubMed:36088121 ]
Liu X, Li Y, Micallef SA: Developmentally related and drought-induced shifts in the kale metabolome limited Salmonella enterica association, providing novel insights to enhance food safety. Food Microbiol. 2022 Dec;108:104113. doi: 10.1016/j.fm.2022.104113. Epub 2022 Aug 18. [PubMed:36088120 ]
Tsuda Y, Atta-ur-Rahman, Akhtar MN, Sener B, Parvez M, Sashida Y, Mimaki Y, Mizuno M: The structure of a new crystalline cevane alkaloid: its identity with persicanidine B and harepermine. Nat Prod Res. 2004 Jun;18(3):205-9. doi: 10.1080/14786410410001708990. [PubMed:15143828 ]
LOTUS database [Link]

Showing NP-Card for (1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol (NP0243384)

MOL for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

3D MOL for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

3D SDF for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

3D-SDF for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

PDB for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

3D PDB for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

SMILES for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

INCHI for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

Structure for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)

3D Structure for NP0243384 ((1r,2s,6r,9s,11r,14s,15s,17r,18s,20s,23r,24s)-6,10,23-trimethyl-4-azahexacyclo[12.11.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁴.0¹⁸,²³]pentacosane-17,20-diol)