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Showing NP-Card for β-D-xylopyranose (NP0339498)

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Record Information
Version2.0
Created at2024-09-11 22:08:06 UTC
Updated at2024-09-11 22:08:06 UTC
NP-MRD IDNP0339498
Secondary Accession NumbersNone
Natural Product Identification
Common Nameβ-D-xylopyranose
Descriptionβ-D-xylopyranose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. β-D-xylopyranose is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, β-D-xylopyranose has been detected, but not quantified in, several different foods, such as yams, sago palms, biscuits, oregon yampahs, and abiyuchs. This could make β-D-xylopyranose a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339498 (β-D-xylopyranose)

 
  Mrv1652303202019012D          
 
 10 10  0  0  1  0            999 V2000
   10.8495   -9.1013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5642   -8.6854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.1348   -8.6854    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.8495   -9.9219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5642   -7.8649    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2788   -9.1013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1348   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4315   -9.1013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8495   -7.4527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2788   -7.4527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  3  8  1  6  0  0  0
  5  9  1  0  0  0  0
  5 10  1  1  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for NP0339498 (β-D-xylopyranose)

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3D SDF for NP0339498 (β-D-xylopyranose)
 
  Mrv1652303202019012D          
 
 10 10  0  0  1  0            999 V2000
   10.8495   -9.1013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5642   -8.6854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.1348   -8.6854    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.8495   -9.9219    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5642   -7.8649    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2788   -9.1013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1348   -7.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4315   -9.1013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8495   -7.4527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2788   -7.4527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  3  8  1  6  0  0  0
  5  9  1  0  0  0  0
  5 10  1  1  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0339498

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5-/m1/s1

> <INCHI_KEY>
SRBFZHDQGSBBOR-KKQCNMDGSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.433270181341882

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.786263151759016

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.31062424774241

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265718350182684

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.960899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-xylose

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339498 (β-D-xylopyranose)
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PDB for NP0339498 (β-D-xylopyranose)
HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0      20.252 -16.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.586 -16.213   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.918 -16.213   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      20.252 -18.521   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      21.586 -14.681   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      22.920 -16.989   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      18.918 -14.681   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      17.606 -16.989   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      20.252 -13.912   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      22.920 -13.912   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2    9   10                                                  
CONECT    6    2                                                            
CONECT    7    3    9                                                       
CONECT    8    3                                                            
CONECT    9    5    7                                                       
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0339498 (β-D-xylopyranose)
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SMILES for NP0339498 (β-D-xylopyranose)
O[C@@H]1CO[C@@H](O)[C@H](O)[C@H]1O
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INCHI for NP0339498 (β-D-xylopyranose)
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2R,3R,4S,5R)-oxane-2,3,4,5-tetrol
Traditional Nameβ-D-xylose
CAS Registry NumberNot Available
SMILES
O[C@@H]1CO[C@@H](O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5-/m1/s1
InChI KeySRBFZHDQGSBBOR-KKQCNMDGSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentPentoses  
Alternative Parents
Substituents
  • Pentose 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-2.6ALOGPS
logP-2.3ChemAxon
logS0.91ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.43 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062087  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031294  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02096  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound125409  
PDB IDNot Available
ChEBI ID28161  
Good Scents IDNot Available
References
General ReferencesNot Available