NP-MRD: Showing NP-Card for Spiramine B (NP0067260)

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Record Information

Version

2.0

Created at

2022-04-28 11:47:19 UTC

Updated at

2022-04-28 11:47:19 UTC

NP-MRD ID

NP0067260

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Spiramine B

Description

(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2²,⁵.0²,⁷.0⁸,¹⁸.0⁸,²¹.0¹³,¹⁷]Tricosan-3-yl acetate belongs to the class of organic compounds known as atisane diterpenoids. These are diterpenoids with a structure based on the atisane skeleton, which is a tetracyclic compound containing the [2,2,2]bicyc1ic ring system with the C15-C16 bridge attached at C12. Spiramine B is found in Spiraea japonica, Spiraea japonica var. incisa Yu, Spiraea japonica var. stellaris, Spiraea japonica var.acuminata and Spiraea japonica var.glabra. Based on a literature review very few articles have been published on (1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2²,⁵.0²,⁷.0⁸,¹⁸.0⁸,²¹.0¹³,¹⁷]Tricosan-3-yl acetate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282213472D          

 29 35  0  0  1  0            999 V2000
    6.8471   -0.2747    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1445    0.3270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7072    1.0445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9076    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1888   -0.1328    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0688   -0.3103    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1450   -1.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7611   -1.7669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5584   -1.4989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6138   -0.6570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1074    0.0265    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5720    0.6542    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7333    0.4306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5178    1.2675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0036    1.3574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8056    1.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8698    0.3418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3900   -0.9365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4522   -0.5804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7345   -0.1188    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2994    0.6111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4949    0.7939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0122    1.0845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9321    1.9056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6032    2.3855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5231    3.2066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3543    2.0443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2525    0.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5697    1.4180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  6  0  0  0
  3 14  1  6  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 11 17  1  0  0  0  0
 10 18  1  1  0  0  0
  5 19  1  6  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  4 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  0  0  0  0
  4 29  1  1  0  0  0
M  END


  Mrv1652304282213472D          

 29 35  0  0  1  0            999 V2000
    6.8471   -0.2747    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1445    0.3270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7072    1.0445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9076    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1888   -0.1328    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0688   -0.3103    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1450   -1.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7611   -1.7669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5584   -1.4989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6138   -0.6570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1074    0.0265    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5720    0.6542    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7333    0.4306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.5178    1.2675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0036    1.3574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8056    1.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8698    0.3418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3900   -0.9365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4522   -0.5804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7345   -0.1188    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2994    0.6111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4949    0.7939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0122    1.0845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9321    1.9056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6032    2.3855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5231    3.2066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3543    2.0443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2525    0.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5697    1.4180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  6  0  0  0
  3 14  1  6  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 11 17  1  0  0  0  0
 10 18  1  1  0  0  0
  5 19  1  6  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  4 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  0  0  0  0
  4 29  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0067260

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1C(=C)[C@H]2CC[C@]11[C@H]3C[C@@H]4[C@@]5(C)CCC[C@]4([C@@H]1C2)[C@H](O3)N1CCO[C@H]51

> <INCHI_IDENTIFIER>
InChI=1S/C24H33NO4/c1-13-15-5-8-24(19(13)28-14(2)26)17(11-15)23-7-4-6-22(3)16(23)12-18(24)29-21(23)25-9-10-27-20(22)25/h15-21H,1,4-12H2,2-3H3/t15-,16+,17-,18+,19-,20+,21-,22+,23-,24-/m0/s1

> <INCHI_KEY>
ZPELMDXCJZDIBP-SZAZYLQYSA-N

> <FORMULA>
C24H33NO4

> <MOLECULAR_WEIGHT>
399.531

> <EXACT_MASS>
399.240958547

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
36.27702028554828

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2^{2,5}.0^{2,7}.0^{8,18}.0^{8,21}.0^{13,17}]tricosan-3-yl acetate

> <ALOGPS_LOGP>
2.36

> <JCHEM_LOGP>
3.322187440666668

> <ALOGPS_LOGS>
-3.79

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.44708037788577

> <JCHEM_POLAR_SURFACE_AREA>
48.0

> <JCHEM_REFRACTIVITY>
106.0217

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.47e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2^{2,5}.0^{2,7}.0^{8,18}.0^{8,21}.0^{13,17}]tricosan-3-yl acetate

> <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      12.781  -0.513   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.470   0.610   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.653   1.950   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.161   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.686  -0.248   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.328  -0.579   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.471  -2.206   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.621  -3.298   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.109  -2.798   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.212  -1.226   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.134   0.050   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      14.134   1.221   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      12.569   0.804   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      12.166   2.366   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      14.940   2.534   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.437   2.173   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      16.557   0.638   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      15.661  -1.748   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.311  -1.083   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.971  -0.222   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.159   1.141   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.657   1.482   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.489   2.024   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.340   3.557   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       8.593   4.453   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.443   5.986   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.995   3.816   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.938   1.015   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.530   2.647   0.000  0.00  0.00           C+0
CONECT    1    2    6   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5   23   29                                             
CONECT    5    4    6   19                                                  
CONECT    6    5    1    7   13                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    1   11   18                                             
CONECT   11   10   12   17                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12    6   14                                                  
CONECT   14   13    3                                                       
CONECT   15   12   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   11                                                       
CONECT   18   10                                                            
CONECT   19    5   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    4   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   20   29                                                       
CONECT   29   28    4                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   70    0
END

View in JSmol

Synonyms

Value	Source
(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-Methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2,.0,.0,.0,.0,]tricosan-3-yl acetic acid	Generator

Chemical Formula

C₂₄H₃₃NO₄

Average Mass

399.5310 Da

Monoisotopic Mass

399.24096 Da

IUPAC Name

(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2^{2,5}.0^{2,7}.0^{8,18}.0^{8,21}.0^{13,17}]tricosan-3-yl acetate

Traditional Name

(1R,2S,3S,5S,7R,8R,12R,13R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.2^{2,5}.0^{2,7}.0^{8,18}.0^{8,21}.0^{13,17}]tricosan-3-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1C(=C)[C@H]2CC[C@]11[C@H]3C[C@@H]4[C@@]5(C)CCC[C@]4([C@@H]1C2)[C@H](O3)N1CCO[C@H]51

InChI Identifier

InChI=1S/C24H33NO4/c1-13-15-5-8-24(19(13)28-14(2)26)17(11-15)23-7-4-6-22(3)16(23)12-18(24)29-21(23)25-9-10-27-20(22)25/h15-21H,1,4-12H2,2-3H3/t15-,16+,17-,18+,19-,20+,21-,22+,23-,24-/m0/s1

InChI Key

ZPELMDXCJZDIBP-SZAZYLQYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Spiraea japonica	LOTUS Database	35616633
Spiraea japonica var. incisa Yu	Plant	KNApSAcK
Spiraea japonica var. stellaris	Plant	KNApSAcK
Spiraea japonica var.acuminata	Plant	KNApSAcK
Spiraea japonica var.glabra	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as atisane diterpenoids. These are diterpenoids with a structure based on the atisane skeleton, which is a tetracyclic compound containing the [2,2,2]bicyc1ic ring system with the C15-C16 bridge attached at C12.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Atisane diterpenoids

Alternative Parents

Substituents

Atisane diterpenoid
Alkaloid or derivatives
Piperidine
Oxane
Oxazolidine
Hemiaminal
Carboxylic acid ester
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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	2.36	ALOGPS
logP	3.32	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Basic)	5.45	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	48 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	106.02 m³·mol⁻¹	ChemAxon
Polarizability	36.28 Å³	ChemAxon
Number of Rings	7	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

162822807

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Spiramine B (NP0067260)

MOL for NP0067260 (Spiramine B)

3D MOL for NP0067260 (Spiramine B)

3D SDF for NP0067260 (Spiramine B)

3D-SDF for NP0067260 (Spiramine B)

PDB for NP0067260 (Spiramine B)

3D PDB for NP0067260 (Spiramine B)

SMILES for NP0067260 (Spiramine B)

INCHI for NP0067260 (Spiramine B)

Structure for NP0067260 (Spiramine B)

3D Structure for NP0067260 (Spiramine B)