NP-MRD: Showing NP-Card for (2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione (NP0320022)

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Record Information

Version

2.0

Created at

2022-09-11 21:22:06 UTC

Updated at

2022-09-11 21:22:06 UTC

NP-MRD ID

NP0320022

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione

Description

Tuberostemospironine belongs to the class of organic compounds known as tuberostemospironine-type alkaloids. These are alkaloids with a structure that is characterized by a 2H-spiro[furan-2,9A[9H]pyrrolo[1,2-a]azepin]-\n5-one nucleus which displays a spiro gamma-lactone at C-9 of the basic ring. (2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione is found in Stemona tuberosa. (2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione was first documented in 2006 (PMID: 16300811). Based on a literature review very few articles have been published on Tuberostemospironine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    3.8163   -0.7026    0.3753 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3320   -0.8331    0.5788 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7843   -1.8247   -0.3639 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1237   -3.0296   -0.4258 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8500   -1.2066   -1.1515 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3315   -0.0707   -0.4418 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2295    0.8581   -1.4645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2481    2.2759   -0.9607 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3344    2.4923    0.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4124    1.4561   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9584    0.1567    0.4550 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9114   -0.7999    0.9062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0561   -0.5581    1.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3970   -2.1544    0.7030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9502   -1.9544    0.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6779   -0.4599    0.5773 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5966    0.4526    0.2035 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3513    1.1637    1.3682 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3270   -1.3903    1.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1126   -1.0253   -0.6647 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2019    0.3079    0.5304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0889   -1.1295    1.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3379    0.7972   -2.4291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2562    0.5260   -1.7065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3280    2.9619   -1.8210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7298    2.5153   -0.4651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9879    2.5798    1.0841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8285    3.4744   -0.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2006    1.7964    0.7349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9467    1.3960   -0.9714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5485   -2.8188    1.5723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056   -2.5636   -0.2183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2885   -2.4976    1.1213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6924   -2.3009   -0.6178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2429   -0.2839    1.6041 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1960    1.0674   -0.4828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2213    1.3263    1.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 17  1  0
 17 18  1  0
 17  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 16  1  0
 16 15  1  0
 15 14  1  0
 14 12  1  0
 12 13  2  0
  6  5  1  6
  5  3  1  0
  3  4  2  0
  3  2  1  0
 16  6  1  0
 12 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
 17 36  1  6
 18 37  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 16 35  1  1
 15 33  1  0
 15 34  1  0
 14 31  1  0
 14 32  1  0
M  END


  Mrv1652309112223222D          

 18 20  0  0  1  0            999 V2000
    4.2759    1.3069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1627    0.4897    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7574   -0.0822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5695    0.0627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3972   -0.8245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5800   -0.7113    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8676   -1.4845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4423   -2.1915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6245   -2.2998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0299   -1.7279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1063   -0.9065    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4628   -0.3902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669   -0.6073    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7550    0.3813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5790    0.3419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7961   -0.4540    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4351    0.1009    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8405    0.6728    0.0000 O   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
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 11  1  1  0  0  0
  6 16  1  0  0  0  0
  6 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0320022

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H](O)[C@@]2(CCCCN3[C@H]2CCC3=O)OC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H19NO4/c1-8-11(16)13(18-12(8)17)6-2-3-7-14-9(13)4-5-10(14)15/h8-9,11,16H,2-7H2,1H3/t8-,9-,11-,13-/m0/s1

> <INCHI_KEY>
FPBTZQXLGBERTH-PZEZNAACSA-N

> <FORMULA>
C13H19NO4

> <MOLECULAR_WEIGHT>
253.298

> <EXACT_MASS>
253.131408096

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.962532858722092

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S,4S,9'aS)-3-hydroxy-4-methyl-octahydrospiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione

> <JCHEM_LOGP>
0.1397522463333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.461799403789033

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7629914183995897

> <JCHEM_POLAR_SURFACE_AREA>
66.84

> <JCHEM_REFRACTIVITY>
62.6477

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,9'aS)-3-hydroxy-4-methyl-hexahydro-1'H-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       7.982   2.439   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.770   0.914   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.880  -0.153   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.396   0.117   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       8.208  -1.539   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.683  -1.328   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.220  -2.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.426  -4.091   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.899  -4.293   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.789  -3.225   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.932  -1.692   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.731  -0.728   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.245  -1.134   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.276   0.712   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.814   0.638   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.219  -0.848   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.412   0.188   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.302   1.256   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   16   17                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   11    6                                                  
CONECT   17    6    2   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₉NO₄

Average Mass

253.2980 Da

Monoisotopic Mass

253.13141 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H](O)[C@@]2(CCCCN3[C@H]2CCC3=O)OC1=O

InChI Identifier

InChI=1S/C13H19NO4/c1-8-11(16)13(18-12(8)17)6-2-3-7-14-9(13)4-5-10(14)15/h8-9,11,16H,2-7H2,1H3/t8-,9-,11-,13-/m0/s1

InChI Key

FPBTZQXLGBERTH-PZEZNAACSA-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
Stemona tuberosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tuberostemospironine-type alkaloids. These are alkaloids with a structure that is characterized by a 2H-spiro[furan-2,9A[9H]pyrrolo[1,2-a]azepin]-\n5-one nucleus which displays a spiro gamma-lactone at C-9 of the basic ring.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Stemona alkaloids

Sub Class

Tuberostemospironine-type alkaloids

Direct Parent

Tuberostemospironine-type alkaloids

Alternative Parents

Substituents

Tuberostemospironine backbone
Pyrroloazepine
Azepane
Gamma butyrolactone
Pyrrolidone
2-pyrrolidone
N-alkylpyrrolidine
Oxolane
Pyrrolidine
Tertiary carboxylic acid amide
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Secondary alcohol
Monocarboxylic acid or derivatives
Azacycle
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00029159

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

101449918

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jiang RW, Hon PM, Xu YT, Chan YM, Xu HX, Shaw PC, But PP: Isolation and chemotaxonomic significance of tuberostemospironine-type alkaloids from Stemona tuberosa. Phytochemistry. 2006 Jan;67(1):52-7. doi: 10.1016/j.phytochem.2005.10.004. Epub 2005 Nov 21. [PubMed:16300811 ]
LOTUS database [Link]

Showing NP-Card for (2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione (NP0320022)

MOL for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

3D MOL for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

3D SDF for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

3D-SDF for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

PDB for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

3D PDB for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

SMILES for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

INCHI for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

Structure for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)

3D Structure for NP0320022 ((2s,3s,4s,9'as)-3-hydroxy-4-methyl-hexahydro-1'h-spiro[oxolane-2,9'-pyrrolo[1,2-a]azepine]-3',5-dione)