NP-MRD: Showing NP-Card for Thiobinupharidine (NP0051084)

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Record Information

Version

2.0

Created at

2022-04-27 22:31:08 UTC

Updated at

2022-04-27 22:31:08 UTC

NP-MRD ID

NP0051084

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Thiobinupharidine

Description

Thiobinupharidine belongs to the class of organic compounds known as quinolizines. Quinolizines are compounds containing a quinolizine moiety, which consists of two fused pyridine rings sharing a nitrogen atom. Thiobinupharidine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Thiobinupharidine is found in Nuphar luteum . Thiobinupharidine was first documented in 2003 (PMID: 14643343). Based on a literature review a small amount of articles have been published on Thiobinupharidine (PMID: 31257322) (PMID: 16413779).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200312D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282200312D          

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  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  4 15  1  0  0  0  0
 13 16  1  0  0  0  0
 17 16  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 13 19  1  6  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 17 24  1  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  1  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 29 33  1  0  0  0  0
 25 34  1  6  0  0  0
  3 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051084

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@H](N2C[C@]3(CS[C@]4(C3)CC[C@H]3[C@H](C)CC[C@H](N3C4)C3=COC=C3)CC[C@@H]12)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H42N2O2S/c1-21-3-5-27(23-9-13-33-15-23)31-18-29(11-7-25(21)31)17-30(35-20-29)12-8-26-22(2)4-6-28(32(26)19-30)24-10-14-34-16-24/h9-10,13-16,21-22,25-28H,3-8,11-12,17-20H2,1-2H3/t21-,22-,25+,26+,27+,28+,29+,30+/m1/s1

> <INCHI_KEY>
WBMOHCBEBDKSBI-JYZUVFRYSA-N

> <FORMULA>
C30H42N2O2S

> <MOLECULAR_WEIGHT>
494.74

> <EXACT_MASS>
494.296699774

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
56.92414490211759

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4'S,6S,6''S,9R,9''R,9aS,9''aS)-6,6''-bis(furan-3-yl)-9,9''-dimethyl-hexadecahydrodispiro[quinolizine-3,2'-thiolane-4',3''-quinolizine]

> <ALOGPS_LOGP>
5.35

> <JCHEM_LOGP>
6.163411191

> <ALOGPS_LOGS>
-5.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
9.58324432732105

> <JCHEM_POLAR_SURFACE_AREA>
32.760000000000005

> <JCHEM_REFRACTIVITY>
143.15

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.90e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiobinupharidine

> <JCHEM_VEBER_RULE>
1

$$$$

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      12.158  -0.608   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.008   0.676   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.321   2.054   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.784   2.148   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       9.934   0.864   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      10.621  -0.514   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.771  -1.798   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.310  -3.241   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.105  -4.199   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       7.820  -3.349   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.232  -1.865   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.397   0.958   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.710   2.337   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.560   3.621   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.097   3.527   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.730   1.149   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.297   1.713   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.392   3.250   0.000  0.00  0.00           C+0
HETATM   19  S   UNK     0       6.883   3.636   0.000  0.00  0.00           S+0
HETATM   20  C   UNK     0       3.932   2.425   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       2.633   1.597   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.700   0.059   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.065  -0.653   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.364   0.175   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.401  -0.769   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.035  -0.057   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.032   1.481   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.267   2.309   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.200   3.847   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.084   4.697   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       0.327   6.181   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.866   6.248   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.405   4.806   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.468  -2.307   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.171   3.338   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7                                                       
CONECT   12    5   13                                                       
CONECT   13   12   14   16   19                                             
CONECT   14   13   15                                                       
CONECT   15   14    4                                                       
CONECT   16   13   17                                                       
CONECT   17   16   18   20   24                                             
CONECT   18   17   19                                                       
CONECT   19   18   13                                                       
CONECT   20   17   21                                                       
CONECT   21   20   22   28                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23   17                                                       
CONECT   25   22   26   34                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   21   29                                                  
CONECT   29   28   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   29                                                       
CONECT   34   25                                                            
CONECT   35    3                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₂N₂O₂S

Average Mass

494.7400 Da

Monoisotopic Mass

494.29670 Da

IUPAC Name

(3S,4'S,6S,6''S,9R,9''R,9aS,9''aS)-6,6''-bis(furan-3-yl)-9,9''-dimethyl-hexadecahydrodispiro[quinolizine-3,2'-thiolane-4',3''-quinolizine]

Traditional Name

thiobinupharidine

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@H](N2C[C@]3(CS[C@]4(C3)CC[C@H]3[C@H](C)CC[C@H](N3C4)C3=COC=C3)CC[C@@H]12)C1=COC=C1

InChI Identifier

InChI=1S/C30H42N2O2S/c1-21-3-5-27(23-9-13-33-15-23)31-18-29(11-7-25(21)31)17-30(35-20-29)12-8-26-22(2)4-6-28(32(26)19-30)24-10-14-34-16-24/h9-10,13-16,21-22,25-28H,3-8,11-12,17-20H2,1-2H3/t21-,22-,25+,26+,27+,28+,29+,30+/m1/s1

InChI Key

WBMOHCBEBDKSBI-JYZUVFRYSA-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
Nuphar lutea	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quinolizines. Quinolizines are compounds containing a quinolizine moiety, which consists of two fused pyridine rings sharing a nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolizines

Sub Class

Not Available

Direct Parent

Quinolizines

Alternative Parents

Substituents

Azaspirodecane
Quinolizidine
Quinolizine
Aralkylamine
Piperidine
Furan
Heteroaromatic compound
Thiolane
Tertiary amine
Tertiary aliphatic amine
Oxacycle
Azacycle
Thioether
Dialkylthioether
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Amine
Organic nitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinolizines (CHEBI:9548 )

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	5.35	ALOGPS
logP	6.16	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Basic)	9.58	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	32.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	143.15 m³·mol⁻¹	ChemAxon
Polarizability	56.92 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	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

C00001985

Chemspider ID

390975

KEGG Compound ID

C09990

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442554

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Matsuda H, Morikawa T, Oda M, Asao Y, Yoshikawa M: Potent anti-metastatic activity of dimeric sesquiterpene thioalkaloids from the rhizome of Nuphar pumilum. Bioorg Med Chem Lett. 2003 Dec 15;13(24):4445-9. doi: 10.1016/j.bmcl.2003.09.019. [PubMed:14643343 ]
Matsuda H, Nakamura S, Nakashima S, Fukaya M, Yoshikawa M: Biofunctional Effects of Thiohemiaminal-Type Dimeric Sesquiterpene Alkaloids from Nuphar Plants. Chem Pharm Bull (Tokyo). 2019;67(7):666-674. doi: 10.1248/cpb.c18-01030. [PubMed:31257322 ]
Matsuda H, Yoshida K, Miyagawa K, Nemoto Y, Asao Y, Yoshikawa M: Nuphar alkaloids with immediately apoptosis-inducing activity from Nuphar pumilum and their structural requirements for the activity. Bioorg Med Chem Lett. 2006 Mar 15;16(6):1567-73. doi: 10.1016/j.bmcl.2005.12.032. Epub 2006 Jan 18. [PubMed:16413779 ]

Showing NP-Card for Thiobinupharidine (NP0051084)

MOL for NP0051084 (Thiobinupharidine)

3D MOL for NP0051084 (Thiobinupharidine)

3D SDF for NP0051084 (Thiobinupharidine)

3D-SDF for NP0051084 (Thiobinupharidine)

PDB for NP0051084 (Thiobinupharidine)

3D PDB for NP0051084 (Thiobinupharidine)

SMILES for NP0051084 (Thiobinupharidine)

INCHI for NP0051084 (Thiobinupharidine)

Structure for NP0051084 (Thiobinupharidine)

3D Structure for NP0051084 (Thiobinupharidine)