NP-MRD: Showing NP-Card for trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane (NP0038678)

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Record Information

Version

2.0

Created at

2021-06-20 21:18:10 UTC

Updated at

2021-06-30 00:11:35 UTC

NP-MRD ID

NP0038678

Secondary Accession Numbers

None

Natural Product Identification

Common Name

trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane

Provided By

JEOL Database JEOL Logo

Description

trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane is found in Bruguiera gymnorrhiza. trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane was first documented in 2009 (Huang, X.-Y., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202123183D          

 24 24  0  0  0  0            999 V2000
   -1.9303   -2.9263   -3.0578 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242   -1.5398   -3.2801 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7853   -0.6682   -2.7623 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9629   -0.7855   -0.9395 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3170    1.1584   -0.3668 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7008    1.9931   -0.6125 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5314    1.3445    0.1428 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6553    1.6682    1.5379 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8194    1.8791   -0.3585 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7082    0.8190   -1.5758 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.3614    0.4432   -3.0843 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2340   -1.2387   -2.6891 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1684   -3.0288   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5750   -1.4238   -4.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7280   -1.0245   -3.1911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6470    0.3711   -3.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5255    2.0493   -1.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8384    3.0219   -0.2602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5324    0.2538    0.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5050    1.2950    1.8397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7154    2.8810   -0.7903 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5074    1.9891    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2320   -1.4087   -1.6083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881   -1.9531   -3.1018 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  4  1  0  0  0  0
  2 14  1  6  0  0  0
 10  9  1  0  0  0  0
  4  3  1  0  0  0  0
 11 12  1  0  0  0  0
  5  6  1  0  0  0  0
  3  2  1  0  0  0  0
  6  7  1  0  0  0  0
  7  9  1  0  0  0  0
  2 12  1  0  0  0  0
  7  8  1  0  0  0  0
 10 11  1  0  0  0  0
  7 19  1  1  0  0  0
 12 23  1  0  0  0  0
 12 24  1  0  0  0  0
  3 15  1  0  0  0  0
  3 16  1  0  0  0  0
  1 13  1  0  0  0  0
  9 21  1  0  0  0  0
  9 22  1  0  0  0  0
  6 17  1  0  0  0  0
  6 18  1  0  0  0  0
  8 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0038678

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])C([H])([H])SSC([H])([H])[C@]([H])(O[H])C([H])([H])SSC1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2S4/c7-5-1-9-10-3-6(8)4-12-11-2-5/h5-8H,1-4H2/t5-,6-

> <INCHI_KEY>
PDDAWBKYAQATSA-IZLXSQMJSA-N

> <FORMULA>
C6H12O2S4

> <MOLECULAR_WEIGHT>
244.4

> <EXACT_MASS>
243.972014322

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
23.131713323357733

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4r,9r)-1,2,6,7-tetrathiecane-4,9-diol

> <ALOGPS_LOGP>
1.03

> <JCHEM_LOGP>
0.0786887586666671

> <ALOGPS_LOGS>
-2.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.738351522787209

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.134326098082273

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0457752445953883

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
62.6118

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4r,9r)-1,2,6,7-tetrathiecane-4,9-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  O   UNK     0      -1.930  -2.926  -3.058  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.624  -1.540  -3.280  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.785  -0.668  -2.762  0.00  0.00           C+0
HETATM    4  S   UNK     0      -2.963  -0.786  -0.940  0.00  0.00           S+0
HETATM    5  S   UNK     0      -3.317   1.158  -0.367  0.00  0.00           S+0
HETATM    6  C   UNK     0      -1.701   1.993  -0.613  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.531   1.345   0.143  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.655   1.668   1.538  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.819   1.879  -0.359  0.00  0.00           C+0
HETATM   10  S   UNK     0       1.708   0.819  -1.576  0.00  0.00           S+0
HETATM   11  S   UNK     0       0.361   0.443  -3.084  0.00  0.00           S+0
HETATM   12  C   UNK     0      -0.234  -1.239  -2.689  0.00  0.00           C+0
HETATM   13  H   UNK     0      -2.168  -3.029  -2.117  0.00  0.00           H+0
HETATM   14  H   UNK     0      -1.575  -1.424  -4.370  0.00  0.00           H+0
HETATM   15  H   UNK     0      -3.728  -1.024  -3.191  0.00  0.00           H+0
HETATM   16  H   UNK     0      -2.647   0.371  -3.072  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.526   2.049  -1.688  0.00  0.00           H+0
HETATM   18  H   UNK     0      -1.838   3.022  -0.260  0.00  0.00           H+0
HETATM   19  H   UNK     0      -0.532   0.254   0.086  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.505   1.295   1.840  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.715   2.881  -0.790  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.507   1.989   0.488  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.232  -1.409  -1.608  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.488  -1.953  -3.102  0.00  0.00           H+0
CONECT    1    2   13                                                       
CONECT    2    1   14    3   12                                             
CONECT    3    4    2   15   16                                             
CONECT    4    5    3                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   17   18                                             
CONECT    7    6    9    8   19                                             
CONECT    8    7   20                                                       
CONECT    9   10    7   21   22                                             
CONECT   10    9   11                                                       
CONECT   11   12   10                                                       
CONECT   12   11    2   23   24                                             
CONECT   13    1                                                            
CONECT   14    2                                                            
CONECT   15    3                                                            
CONECT   16    3                                                            
CONECT   17    6                                                            
CONECT   18    6                                                            
CONECT   19    7                                                            
CONECT   20    8                                                            
CONECT   21    9                                                            
CONECT   22    9                                                            
CONECT   23   12                                                            
CONECT   24   12                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₆H₁₂O₂S₄

Average Mass

244.4000 Da

Monoisotopic Mass

243.97201 Da

IUPAC Name

(4r,9r)-1,2,6,7-tetrathiecane-4,9-diol

Traditional Name

(4r,9r)-1,2,6,7-tetrathiecane-4,9-diol

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])C([H])([H])SSC([H])([H])[C@]([H])(O[H])C([H])([H])SSC1([H])[H]

InChI Identifier

InChI=1S/C6H12O2S4/c7-5-1-9-10-3-6(8)4-12-11-2-5/h5-8H,1-4H2/t5-,6-

InChI Key

PDDAWBKYAQATSA-IZLXSQMJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, C₅D₅N, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Bruguiera gymnorhiza	JEOL database	Huang, X.-Y., et al, Phytochemistry 70, 2096 (2009)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Secondary alcohols

Alternative Parents

Substituents

Secondary alcohol
Organic disulfide
Organoheterocyclic compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	1.03	ALOGPS
logP	0.079	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	14.13	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	62.61 m³·mol⁻¹	ChemAxon
Polarizability	23.13 Å³	ChemAxon
Number of Rings	1	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

27024668

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Huang, X.-Y., et al. (2009). Huang, X.-Y., et al, Phytochemistry 70, 2096 (2009). Phytochem..

Showing NP-Card for trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane (NP0038678)

MOL for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

3D MOL for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

3D SDF for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

3D-SDF for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

PDB for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

3D PDB for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

SMILES for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

INCHI for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

Structure for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)

3D Structure for NP0038678 (trans-3,3'-dihydroxy-1,5,10,5'-tetrathiacyclodecane)