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Showing NP-Card for xi-2-Methyl-1,3-oxathiane (NP0049504)

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Record Information
Version2.0
Created at2022-03-17 21:13:35 UTC
Updated at2022-03-17 21:13:35 UTC
NP-MRD IDNP0049504
Secondary Accession NumbersNone
Natural Product Identification
Common Namexi-2-Methyl-1,3-oxathiane
DescriptionXi-2-Methyl-1,3-oxathiane belongs to the class of organic compounds known as oxathianes. Oxathianes are compounds containing an oxathiane moiety, which consists of a saturated aliphatic six-member ring with one oxygen atom, a sulfur atom, and four carbon atoms. Isomers of oxaphospholane include 1,2-oxathiane, 1,3-oxathiane,and 1,4-oxathiane. Xi-2-Methyl-1,3-oxathiane is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, xi-2-Methyl-1,3-oxathiane has been detected, but not quantified in, onion-family vegetables. This could make XI-2-methyl-1,3-oxathiane a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049504 (xi-2-Methyl-1,3-oxathiane)


  Mrv0541 05061311252D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
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3D MOL for NP0049504 (xi-2-Methyl-1,3-oxathiane)

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3D SDF for NP0049504 (xi-2-Methyl-1,3-oxathiane)

  Mrv0541 05061311252D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049504

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OCCCS1

> <INCHI_IDENTIFIER>
InChI=1S/C5H10OS/c1-5-6-3-2-4-7-5/h5H,2-4H2,1H3

> <INCHI_KEY>
VKZBKCJAWXBYBF-UHFFFAOYSA-N

> <FORMULA>
C5H10OS

> <MOLECULAR_WEIGHT>
118.197

> <EXACT_MASS>
118.045235632

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
12.885195365525172

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methyl-1,3-oxathiane

> <ALOGPS_LOGP>
1.38

> <JCHEM_LOGP>
0.9128557946666664

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.214375880107641

> <JCHEM_POLAR_SURFACE_AREA>
9.23

> <JCHEM_REFRACTIVITY>
32.7736

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.11e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-1,3-oxathiane

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0049504 (xi-2-Methyl-1,3-oxathiane)
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PDB for NP0049504 (xi-2-Methyl-1,3-oxathiane)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    7  S   UNK     0       0.000   1.540   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2    7                                                       
CONECT    5    1    6    7                                                  
CONECT    6    3    5                                                       
CONECT    7    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END

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3D PDB for NP0049504 (xi-2-Methyl-1,3-oxathiane)
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SMILES for NP0049504 (xi-2-Methyl-1,3-oxathiane)
CC1OCCCS1
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INCHI for NP0049504 (xi-2-Methyl-1,3-oxathiane)
InChI=1S/C5H10OS/c1-5-6-3-2-4-7-5/h5H,2-4H2,1H3
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SynonymsNot Available
Chemical FormulaC5H10OS
Average Mass118.1970 Da
Monoisotopic Mass118.04524 Da
IUPAC Name2-methyl-1,3-oxathiane
Traditional Name2-methyl-1,3-oxathiane
CAS Registry NumberNot Available
SMILES
CC1OCCCS1
InChI Identifier
InChI=1S/C5H10OS/c1-5-6-3-2-4-7-5/h5H,2-4H2,1H3
InChI KeyVKZBKCJAWXBYBF-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Allium cepaFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Allium fistulosumFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxathianes. Oxathianes are compounds containing an oxathiane moiety, which consists of a saturated aliphatic six-member ring with one oxygen atom, a sulfur atom, and four carbon atoms. Isomers  of oxaphospholane include 1,2-oxathiane, 1,3-oxathiane,and 1,4-oxathiane.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassOxathianes  
Sub ClassNot Available
Direct ParentOxathianes  
Alternative Parents
Substituents
  • 1,3-oxathiane
    • 

  • Monothioacetal
    • 

  • Oxacycle
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.38ALOGPS
logP0.91ChemAxon
logS-1.1ALOGPS
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area9.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.77 m³·mol⁻¹ChemAxon
Polarizability12.89 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0039826  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB019479  
KNApSAcK IDNot Available
Chemspider ID472581  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound542685  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available