NP-MRD: Showing NP-Card for Spirolucidine (NP0051060)

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Record Information

Version

2.0

Created at

2022-04-27 22:30:12 UTC

Updated at

2022-04-27 22:30:12 UTC

NP-MRD ID

NP0051060

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Spirolucidine

Description

Spirolucidine belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom. Spirolucidine is found in Huperzia lucidula, Lycopodium lucidulum and Lycopodium lucidum. Spirolucidine was first documented in 2001 (PMID: 11574035). Based on a literature review very few articles have been published on spirolucidine.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200302D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282200302D          

 35 40  0  0  1  0            999 V2000
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    6.0093   -4.9030    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7401   -5.6828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2809   -6.3059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9302   -5.8396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3079   -3.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  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
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  8 14  1  0  0  0  0
 10 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 19 18  1  6  0  0  0
 10 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  1  0  0  0
 17 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 16 25  1  0  0  0  0
 24 26  1  6  0  0  0
 21 27  1  0  0  0  0
  5 28  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
  4 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
  2 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0051060

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@H](C[C@H]2CCC(=O)[C@@]3(C[C@@H]4C[C@@H](C)C[C@H]5[C@@H]4C[C@@H]3CN5C)N2)[C@H]2CCCN([C@H]2C1)C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H49N3O2/c1-18-10-21(25-6-5-9-33(20(3)34)28(25)13-18)14-24-7-8-29(35)30(31-24)16-22-11-19(2)12-27-26(22)15-23(30)17-32(27)4/h18-19,21-28,31H,5-17H2,1-4H3/t18-,19+,21+,22-,23+,24+,25+,26+,27-,28-,30-/m0/s1

> <INCHI_KEY>
DOAGKNAZGHOTJU-PALKDTOHSA-N

> <FORMULA>
C30H49N3O2

> <MOLECULAR_WEIGHT>
483.741

> <EXACT_MASS>
483.38247783

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
57.54182082782263

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2S,4'S,6R,6'R,8'S,9'R)-6-{[(4aR,5R,7S,8aS)-1-acetyl-7-methyl-decahydroquinolin-5-yl]methyl}-6',12'-dimethyl-12'-azaspiro[piperidine-2,2'-tricyclo[6.2.2.0^{4,9}]dodecane]-3-one

> <ALOGPS_LOGP>
3.69

> <JCHEM_LOGP>
3.756644786000001

> <ALOGPS_LOGS>
-5.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.673119138396835

> <JCHEM_PKA_STRONGEST_BASIC>
9.586713998469104

> <JCHEM_POLAR_SURFACE_AREA>
52.650000000000006

> <JCHEM_REFRACTIVITY>
140.33379999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.34e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2S,4'S,6R,6'R,8'S,9'R)-6-{[(4aR,5R,7S,8aS)-1-acetyl-7-methyl-octahydro-2H-quinolin-5-yl]methyl}-6',12'-dimethyl-12'-azaspiro[piperidine-2,2'-tricyclo[6.2.2.0^{4,9}]dodecane]-3-one

> <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       8.189  -5.663   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.687  -7.119   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.696  -8.282   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.208  -7.989   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.711  -6.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.701  -5.370   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.204  -3.915   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.194  -2.752   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       7.682  -3.044   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       6.673  -1.881   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.175  -0.426   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.166   0.737   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.687  -0.133   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.697  -1.296   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.663  -0.566   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.054  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.803  -2.248   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.119  -2.952   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.156  -3.493   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.106  -4.821   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       3.445  -4.711   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.700  -3.255   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.314  -2.396   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.238  -0.819   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.608  -0.045   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.110  -0.075   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.598  -5.997   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.222  -6.241   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.232  -7.404   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.729  -8.860   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      11.217  -9.152   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      10.715 -10.608   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      11.724 -11.771   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.203 -10.901   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.175  -7.412   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   31                                                  
CONECT    5    4    6   28                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   15   19                                             
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8                                                       
CONECT   15   10   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   10   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   17   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24   16                                                       
CONECT   26   24                                                            
CONECT   27   21                                                            
CONECT   28    5   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30    4   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35    2                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₉N₃O₂

Average Mass

483.7410 Da

Monoisotopic Mass

483.38248 Da

IUPAC Name

(1'R,2S,4'S,6R,6'R,8'S,9'R)-6-{[(4aR,5R,7S,8aS)-1-acetyl-7-methyl-decahydroquinolin-5-yl]methyl}-6',12'-dimethyl-12'-azaspiro[piperidine-2,2'-tricyclo[6.2.2.0^{4,9}]dodecane]-3-one

Traditional Name

(1'R,2S,4'S,6R,6'R,8'S,9'R)-6-{[(4aR,5R,7S,8aS)-1-acetyl-7-methyl-octahydro-2H-quinolin-5-yl]methyl}-6',12'-dimethyl-12'-azaspiro[piperidine-2,2'-tricyclo[6.2.2.0^{4,9}]dodecane]-3-one

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@H](C[C@H]2CCC(=O)[C@@]3(C[C@@H]4C[C@@H](C)C[C@H]5[C@@H]4C[C@@H]3CN5C)N2)[C@H]2CCCN([C@H]2C1)C(C)=O

InChI Identifier

InChI=1S/C30H49N3O2/c1-18-10-21(25-6-5-9-33(20(3)34)28(25)13-18)14-24-7-8-29(35)30(31-24)16-22-11-19(2)12-27-26(22)15-23(30)17-32(27)4/h18-19,21-28,31H,5-17H2,1-4H3/t18-,19+,21+,22-,23+,24+,25+,26+,27-,28-,30-/m0/s1

InChI Key

DOAGKNAZGHOTJU-PALKDTOHSA-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
Huperzia lucidula	LOTUS Database	35616633
Lycopodium lucidulum	Plant	KNApSAcK
Lycopodium lucidum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as azaspirodecane derivatives. These are organic compounds containing a spirodecane moiety with at least one nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azaspirodecane derivatives

Sub Class

Not Available

Direct Parent

Azaspirodecane derivatives

Alternative Parents

Substituents

Azaspirodecane
Quinolidine
N-acyl-piperidine
Piperidinone
Piperidine
Tertiary carboxylic acid amide
Acetamide
Tertiary aliphatic amine
Amino acid or derivatives
Tertiary amine
Carboxamide group
Ketone
Azacycle
Secondary amine
Carboxylic acid derivative
Secondary aliphatic amine
Hydrocarbon derivative
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

piperidines (CHEBI:9240 )
azaspiro compound (CHEBI:9240 )
decahydroquinoline alkaloid (CHEBI:9240 )

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	3.69	ALOGPS
logP	3.76	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	17.67	ChemAxon
pKa (Strongest Basic)	9.59	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	52.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	140.33 m³·mol⁻¹	ChemAxon
Polarizability	57.54 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

C00001959

Chemspider ID

390928

KEGG Compound ID

C09903

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442502

PDB ID

Not Available

ChEBI ID

9240

Good Scents ID

Not Available

References

General References

Comins DL, Williams AL: Model studies toward the total synthesis of the Lycopodium alkaloid spirolucidine. Org Lett. 2001 Oct 4;3(20):3217-20. doi: 10.1021/ol016556o. [PubMed:11574035 ]

Showing NP-Card for Spirolucidine (NP0051060)

MOL for NP0051060 (Spirolucidine)

3D MOL for NP0051060 (Spirolucidine)

3D SDF for NP0051060 (Spirolucidine)

3D-SDF for NP0051060 (Spirolucidine)

PDB for NP0051060 (Spirolucidine)

3D PDB for NP0051060 (Spirolucidine)

SMILES for NP0051060 (Spirolucidine)

INCHI for NP0051060 (Spirolucidine)

Structure for NP0051060 (Spirolucidine)

3D Structure for NP0051060 (Spirolucidine)