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Showing NP-Card for 3,6-dideoxy-d-xylo-hexose (NP0250828)

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Record Information
Version1.0
Created at2022-09-07 13:47:58 UTC
Updated at2022-09-07 13:47:58 UTC
NP-MRD IDNP0250828
Secondary Accession NumbersNone
Natural Product Identification
Common Name3,6-dideoxy-d-xylo-hexose
Description3,6-Didesoxyhexos belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity. 3,6-dideoxy-d-xylo-hexose is found in Bacterium. 3,6-Didesoxyhexos is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0250828 (3,6-dideoxy-d-xylo-hexose)


  Mrv1533004151519132D          

 10 10  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    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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   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
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   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
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0250828 (3,6-dideoxy-d-xylo-hexose)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
    2.4765    0.0938    0.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2669   -0.2457   -0.0922 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4983   -1.1302    0.6614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6967   -1.4100   -0.0102 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3596   -2.4922    0.5107 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5235   -0.1211    0.0786 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8447   -0.3325   -0.2190 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8486    0.8514   -0.8898 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5611    1.0324   -0.4135 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5220    1.8788    0.7017 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0633    0.4740    1.7570 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1261    0.8399    0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0007   -0.8639    1.0209 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6897   -0.7368   -0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4040   -1.5486   -1.0863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4998   -3.1433   -0.2377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4311    0.3402    1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4382    0.0039    0.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9351    0.4618   -1.9150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3727    1.8276   -0.7887 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1467    1.5398   -1.2193 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0028    2.6806    0.4070 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
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  4 15  1  6
  5 16  1  0
  6 17  1  1
  7 18  1  0
  8 19  1  0
  8 20  1  0
  9 21  1  6
 10 22  1  0
M  END
Download

3D SDF for NP0250828 (3,6-dideoxy-d-xylo-hexose)


  Mrv1533004151519132D          

 10 10  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    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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   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
    0.7145   -1.2375    0.0000 O   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
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   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
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0250828

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(O)C(O)CC1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O4/c1-3-4(7)2-5(8)6(9)10-3/h3-9H,2H2,1H3

> <INCHI_KEY>
KYPWIZMAJMNPMJ-UHFFFAOYSA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.158

> <EXACT_MASS>
148.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.495456158843087

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-methyloxane-2,3,5-triol

> <ALOGPS_LOGP>
-1.73

> <JCHEM_LOGP>
-1.1953345703333336

> <ALOGPS_LOGS>
0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.86966577993596

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.433746026821177

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1878166539528996

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
33.2826

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.48e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,6-dideoxy-D-xylo-hexose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0250828 (3,6-dideoxy-d-xylo-hexose)

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PDB for NP0250828 (3,6-dideoxy-d-xylo-hexose)
HEADER    PROTEIN                                 15-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-APR-15         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   2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0250828 (3,6-dideoxy-d-xylo-hexose)
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SMILES for NP0250828 (3,6-dideoxy-d-xylo-hexose)
CC1OC(O)C(O)CC1O
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INCHI for NP0250828 (3,6-dideoxy-d-xylo-hexose)
InChI=1S/C6H12O4/c1-3-4(7)2-5(8)6(9)10-3/h3-9H,2H2,1H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H12O4
Average Mass148.1580 Da
Monoisotopic Mass148.07356 Da
IUPAC Name6-methyloxane-2,3,5-triol
Traditional Name3,6-dideoxy-D-xylo-hexose
CAS Registry NumberNot Available
SMILES
CC1OC(O)C(O)CC1O
InChI Identifier
InChI=1S/C6H12O4/c1-3-4(7)2-5(8)6(9)10-3/h3-9H,2H2,1H3
InChI KeyKYPWIZMAJMNPMJ-UHFFFAOYSA-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
Bacterium; sewage; soilLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentHexoses  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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-1.7ALOGPS
logP-1.2ChemAxon
logS0.76ALOGPS
pKa (Strongest Acidic)11.43ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.28 m³·mol⁻¹ChemAxon
Polarizability14.5 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4471182  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]