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Showing NP-Card for (2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol (NP0198402)

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Record Information
Version2.0
Created at2022-09-04 16:50:51 UTC
Updated at2022-09-04 16:50:51 UTC
NP-MRD IDNP0198402
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol
Description1,4-Dideoxy-1,4-epithio-d-arabinitol belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom. (2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol is found in Salacia chinensis. (2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol was first documented in 2006 (PMID: 16198577). Based on a literature review very few articles have been published on 1,4-dideoxy-1,4-epithio-d-arabinitol (PMID: 19307117).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)


  Mrv1652309042218502D          

  9  9  0  0  1  0            999 V2000
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  6  0  0  0
M  END
Download

3D MOL for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)

     RDKit          3D

 19 19  0  0  0  0  0  0  0  0999 V2000
    2.3939   -0.1127    1.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1664   -0.4176   -0.2804 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7064   -0.6125   -0.6102 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0003   -1.9850    0.3809 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6078   -1.1776    0.7419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5267    0.1251    0.0125 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1771    1.0789    0.8283 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1161    0.5362   -0.1282 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0552    1.5283   -1.1348 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2283    0.4482    1.0794 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5212    0.4294   -0.8993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7102   -1.3197   -0.6249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6016   -0.8563   -1.6654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7965   -1.1014    1.8129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3752   -1.8057    0.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0528    0.1472   -0.9503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5081    1.8360    0.3074 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3528    0.9280    0.7993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4657    2.3312   -0.7697 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  5 14  1  0
  5 15  1  0
  6 16  1  6
  7 17  1  0
  8 18  1  1
  9 19  1  0
M  END
Download

3D SDF for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)


  Mrv1652309042218502D          

  9  9  0  0  1  0            999 V2000
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0198402

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1SC[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3S/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4-,5+/m1/s1

> <INCHI_KEY>
VLVSFIRYIVAVKW-WDCZJNDASA-N

> <FORMULA>
C5H10O3S

> <MOLECULAR_WEIGHT>
150.19

> <EXACT_MASS>
150.035065356

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.43403901286733

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S)-2-(hydroxymethyl)thiolane-3,4-diol

> <JCHEM_LOGP>
-1.4984960836666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.656837444892492

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.36782608018492

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7956374818250094

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
35.244

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S)-2-(hydroxymethyl)thiolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)

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PDB for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)
HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       2.306   1.175   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    3    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)
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SMILES for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)
OC[C@H]1SC[C@@H](O)[C@@H]1O
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INCHI for NP0198402 ((2r,3s,4s)-2-(hydroxymethyl)thiolane-3,4-diol)
InChI=1S/C5H10O3S/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4-,5+/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H10O3S
Average Mass150.1900 Da
Monoisotopic Mass150.03507 Da
IUPAC Name(2R,3S,4S)-2-(hydroxymethyl)thiolane-3,4-diol
Traditional Name(2R,3S,4S)-2-(hydroxymethyl)thiolane-3,4-diol
CAS Registry NumberNot Available
SMILES
OC[C@H]1SC[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O3S/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4-,5+/m1/s1
InChI KeyVLVSFIRYIVAVKW-WDCZJNDASA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Salacia chinensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiolanes. These are organic compounds containing thiolane, a five-member saturated ring containing four carbon atoms and a sulfur atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassThiolanes  
Sub ClassNot Available
Direct ParentThiolanes  
Alternative Parents
Substituents
  • Thiolane
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Dialkylthioether
    • 

  • Thioether
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • 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
logP-1.5ChemAxon
pKa (Strongest Acidic)13.37ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.24 m³·mol⁻¹ChemAxon
Polarizability14.43 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9598560  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11423684  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Tanabe G, Xie W, Ogawa A, Cao C, Minematsu T, Yoshikawa M, Muraoka O: Facile synthesis of de-O-sulfated salacinols: revision of the structure of neosalacinol, a potent alpha-glucosidase inhibitor. Bioorg Med Chem Lett. 2009 Apr 15;19(8):2195-8. doi: 10.1016/j.bmcl.2009.02.103.  Epub 2009 Mar 1. [PubMed:19307117  ] 
  2. Muraoka O, Yoshikai K, Takahashi H, Minematsu T, Lu G, Tanabe G, Wang T, Matsuda H, Yoshikawa M: Synthesis and biological evaluation of deoxy salacinols, the role of polar substituents in the side chain on the alpha-glucosidase inhibitory activity. Bioorg Med Chem. 2006 Jan 15;14(2):500-9. doi: 10.1016/j.bmc.2005.08.040. Epub  2005 Sep 29. [PubMed:16198577  ] 
  3. LOTUS database [Link]