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Showing NP-Card for 2-O-b-D-Xylopyranosyl-L-arabinose (NP0338313)

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Record Information
Version2.0
Created at2024-09-11 14:51:47 UTC
Updated at2024-09-11 14:51:47 UTC
NP-MRD IDNP0338313
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-O-b-D-Xylopyranosyl-L-arabinose
Description2-O-b-D-Xylopyranosyl-L-arabinose belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Based on a literature review very few articles have been published on 2-O-b-D-Xylopyranosyl-L-arabinose.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)


  Mrv2104 05262317242D          

 19 20  0  0  0  0            999 V2000
    1.3750    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6605    5.9125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6605    5.0875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3750    4.6750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0895    5.0875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0895    5.9125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8039    4.6750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750    3.8500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0539    4.6750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4540    7.7539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0415    8.4684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2164    8.4684    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8039    7.7539    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2164    7.0395    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0415    7.0395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4539    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8039    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9789    7.7539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8039    9.1829    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
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6 17  1  1  0  0  0
  5  7  1  6  0  0  0
  4  8  1  1  0  0  0
  3  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  6  0  0  0
 13 18  1  1  0  0  0
 12 19  1  1  0  0  0
M  END
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3D MOL for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)

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3D SDF for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)

  Mrv2104 05262317242D          

 19 20  0  0  0  0            999 V2000
    1.3750    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6605    5.9125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6605    5.0875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3750    4.6750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0895    5.0875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0895    5.9125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8039    4.6750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750    3.8500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0539    4.6750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4540    7.7539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0415    8.4684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2164    8.4684    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8039    7.7539    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2164    7.0395    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0415    7.0395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4539    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8039    6.3250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9789    7.7539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8039    9.1829    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
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6 17  1  1  0  0  0
  5  7  1  6  0  0  0
  4  8  1  1  0  0  0
  3  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  6  0  0  0
 13 18  1  1  0  0  0
 12 19  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0338313

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CO[C@@H](O[C@H]2C(O)OC[C@H](O)[C@@H]2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1/C10H18O9/c11-3-2-18-10(7(15)5(3)13)19-8-6(14)4(12)1-17-9(8)16/h3-16H,1-2H2/t3-,4+,5+,6+,7-,8-,9?,10+/s2

> <INCHI_KEY>
HBIRURHHLFDSPS-BCPXLOOFNA-N

> <FORMULA>
C10H18O9

> <MOLECULAR_WEIGHT>
282.245

> <EXACT_MASS>
282.09508216

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.46596367158877

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R)-2-{[(3R,4S,5S)-2,4,5-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

> <JCHEM_LOGP>
-3.442704979666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.208957368185208

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.283360136097716

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265806826121335

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
56.411699999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5R)-2-{[(3R,4S,5S)-2,4,5-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)
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PDB for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)
HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  O   UNK     0       2.567  11.807   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.233  11.037   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.233   9.497   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.567   8.727   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.900   9.497   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.900  11.037   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.234   8.727   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.567   7.187   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.101   8.727   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.314  14.474   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.544  15.808   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.004  15.808   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.234  14.474   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.004  13.140   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.544  13.140   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.314  11.807   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.234  11.807   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.694  14.474   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.234  17.141   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1   17                                                  
CONECT    7    5                                                            
CONECT    8    4                                                            
CONECT    9    3                                                            
CONECT   10   11   15                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   10   16                                                  
CONECT   16   15                                                            
CONECT   17    6   14                                                       
CONECT   18   13                                                            
CONECT   19   12                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

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3D PDB for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)
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SMILES for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)
O[C@@H]1CO[C@@H](O[C@H]2C(O)OC[C@H](O)[C@@H]2O)[C@H](O)[C@H]1O
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INCHI for NP0338313 (2-O-b-D-Xylopyranosyl-L-arabinose)
InChI=1/C10H18O9/c11-3-2-18-10(7(15)5(3)13)19-8-6(14)4(12)1-17-9(8)16/h3-16H,1-2H2/t3-,4+,5+,6+,7-,8-,9?,10+/s2
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View in JSmol
SynonymsNot Available
Chemical FormulaC10H18O9
Average Mass282.2450 Da
Monoisotopic Mass282.09508 Da
IUPAC Name(2S,3R,4S,5R)-2-{[(3R,4S,5S)-2,4,5-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol
Traditional Name(2S,3R,4S,5R)-2-{[(3R,4S,5S)-2,4,5-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
O[C@@H]1CO[C@@H](O[C@H]2C(O)OC[C@H](O)[C@@H]2O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1/C10H18O9/c11-3-2-18-10(7(15)5(3)13)19-8-6(14)4(12)1-17-9(8)16/h3-16H,1-2H2/t3-,4+,5+,6+,7-,8-,9?,10+/s2
InChI KeyHBIRURHHLFDSPS-BCPXLOOFNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentO-glycosyl compounds  
Alternative Parents
Substituents
  • O-glycosyl compound
    • 

  • Disaccharide
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Hydrocarbon derivative
    • 

  • 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-3.4ChemAxon
pKa (Strongest Acidic)11.28ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area149.07 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity56.41 m³·mol⁻¹ChemAxon
Polarizability25.47 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available