NP-MRD: Showing NP-Card for 3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate (NP0283978)

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Record Information

Version

2.0

Created at

2022-09-09 11:28:49 UTC

Updated at

2022-09-09 11:28:49 UTC

NP-MRD ID

NP0283978

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate

Description

CHEMBL460255 belongs to the class of organic compounds known as sulfoxides. Sulfoxides are compounds containing a sulfoxide functional group, with the structure RS(=O)R' (R,R' not H). 3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate is found in Salacia reticulata. Based on a literature review very few articles have been published on CHEMBL460255.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 46 46  0  0  0  0  0  0  0  0999 V2000
   -0.5647    2.9554   -2.1972 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.1496    1.9750   -1.0335 S   0  0  0  0  0  3  0  0  0  0  0  0
   -0.9991    1.7691    0.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2822    1.2971   -0.2167 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1626    2.4069   -0.2588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9745    0.2173    0.5153 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.0709   -0.1965   -0.2720 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1782   -0.9858    0.8441 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8575   -1.6665    1.8856 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0659   -1.9790   -0.2846 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2664   -3.3011    0.1606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7672   -1.8751   -1.0071 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4344   -2.2245   -0.2109 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7478   -3.5917   -0.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6226   -1.4136   -0.7328 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2187   -0.5638    0.3680 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1028   -1.3961    1.0815 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9292    0.6560   -0.1778 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3070    0.4814    0.0793 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4250    1.9078    0.4689 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5510    2.6819    0.8297 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6234    2.7737   -0.4868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0774    2.7988    0.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5079    1.1438    1.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2018    0.9846   -1.2994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9171    3.0506    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4431    0.5968    1.4656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6706    0.5641   -0.4840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1750   -0.7730    1.2701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7108   -2.0433    1.5519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8806   -1.7903   -1.0158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6934   -3.5166    0.9283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6909   -0.8730   -1.4608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8166   -2.5906   -1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3379   -2.0839    0.8783 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4708   -3.6698   -1.0535 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3265   -0.8097   -1.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4359   -2.0851   -1.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4589   -0.2387    1.1101 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7479   -1.7926    0.4420 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8539    0.6889   -1.2958 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4650    0.5228    1.0738 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8575    1.7008    1.3884 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2519    3.5580    1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2398    2.9928   -1.3765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4168    3.7362    0.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22  2  1  0
  2  1  1  6
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 14 36  1  0
 13 35  1  1
 15 37  1  0
 15 38  1  0
 16 39  1  1
 17 40  1  0
 18 41  1  6
 19 42  1  0
 20 43  1  1
 21 44  1  0
 22 45  1  0
 22 46  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  6
  5 26  1  0
  6 27  1  1
  7 28  1  0
  8 29  1  1
  9 30  1  0
 10 31  1  6
 11 32  1  0
 12 33  1  0
 12 34  1  0
M  CHG  2   1  -1   2   1
M  END


  Mrv1652309092213282D          

 22 22  0  0  0  0            999 V2000
    1.6335    1.7356    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9097    0.9582    0.0000 S   0  3  0  0  0  0  0  0  0  0  0  0
    2.5480    1.4809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2423    1.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0109    1.3351    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0331    0.2372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2113    0.1644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4121   -0.5822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2351   -0.6388    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9665   -1.2765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1424   -1.2378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5209   -1.9708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6968   -1.9321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8727   -1.8933    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4271   -2.5877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4942   -1.1603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3299   -1.1216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9398   -0.4660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639   -0.5047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5613    0.2671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2628    0.3058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0069    0.9614    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
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
  2 22  1  0  0  0  0
M  CHG  2   1  -1   2   1
M  END
> <DATABASE_ID>
NP0283978

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1CC(O)C(O)C(O)C[S+]([O-])CC(O)C(O)C(O)C(O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H24O9S/c13-5-1-6(14)10(18)8(16)3-22(21)4-9(17)12(20)11(19)7(15)2-5/h5-20H,1-4H2

> <INCHI_KEY>
ZCFDZGVJJBUOOF-UHFFFAOYSA-N

> <FORMULA>
C12H24O9S

> <MOLECULAR_WEIGHT>
344.38

> <EXACT_MASS>
344.114103527

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
32.45912696360794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate

> <JCHEM_LOGP>
-6.197772213333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.112828801011556

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.56026510265212

> <JCHEM_PKA_STRONGEST_BASIC>
-2.761928385716475

> <JCHEM_POLAR_SURFACE_AREA>
178.91

> <JCHEM_REFRACTIVITY>
76.35239999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  O   UNK     0       3.049   3.240   0.000  0.00  0.00           O-1
HETATM    2  S   UNK     0       3.565   1.789   0.000  0.00  0.00           S+1
HETATM    3  C   UNK     0       4.756   2.764   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.052   1.933   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.487   2.492   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.662   0.443   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.128   0.307   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.369  -1.087   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       7.906  -1.192   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       5.537  -2.383   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.999  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.706  -3.679   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.167  -3.607   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.629  -3.534   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.797  -4.830   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.923  -2.166   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.616  -2.094   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.754  -0.870   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.293  -0.942   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.048   0.499   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.491   0.571   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.879   1.795   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    2                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₄O₉S

Average Mass

344.3800 Da

Monoisotopic Mass

344.11410 Da

IUPAC Name

3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate

Traditional Name

3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate

CAS Registry Number

Not Available

SMILES

OC1CC(O)C(O)C(O)C[S+]([O-])CC(O)C(O)C(O)C(O)C1

InChI Identifier

InChI=1S/C12H24O9S/c13-5-1-6(14)10(18)8(16)3-22(21)4-9(17)12(20)11(19)7(15)2-5/h5-20H,1-4H2

InChI Key

ZCFDZGVJJBUOOF-UHFFFAOYSA-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
Salacia reticulata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sulfoxides. Sulfoxides are compounds containing a sulfoxide functional group, with the structure RS(=O)R' (R,R' not H).

Kingdom

Organic compounds

Super Class

Organosulfur compounds

Class

Sulfoxides

Sub Class

Not Available

Direct Parent

Sulfoxides

Alternative Parents

Substituents

Sulfoxide
Secondary alcohol
Organoheterocyclic compound
Sulfinyl compound
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

sulfoxide (CHEBI:66770 )

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	-6.2	ChemAxon
pKa (Strongest Acidic)	12.56	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	178.91 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	76.35 m³·mol⁻¹	ChemAxon
Polarizability	32.46 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

Not Available

Chemspider ID

23328290

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24808560

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate (NP0283978)

MOL for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

3D MOL for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

3D SDF for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

3D-SDF for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

PDB for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

3D PDB for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

SMILES for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

INCHI for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

Structure for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)

3D Structure for NP0283978 (3,4,5,6,8,10,11,12-octahydroxy-1-thiacyclotridecan-1-ium-1-olate)