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Showing NP-Card for (d)-xylose (NP0326534)

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Record Information
Version1.0
Created at2022-09-12 08:10:43 UTC
Updated at2022-09-12 08:10:43 UTC
NP-MRD IDNP0326534
Secondary Accession NumbersNone
Natural Product Identification
Common Name(d)-xylose
DescriptionXylose, also known as D-xylose or wood sugar, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. The dextrorotary form of xylose, D-xylose, refers usually to the endogenously occurring form of the sugar in living things. Xylose is a sugar widely used as a diabetic sweetener in food and beverage. Xylose is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, xylose is involved in nucleotide sugars metabolism. Xylose is a sweet, caramel, and smoky tasting compound. Outside of the human body, Xylose is found, on average, in the highest concentration within flaxseeds and carobs. Xylose has also been detected, but not quantified in, several different foods, such as cereals and cereal products, red beetroots, ginkgo nuts, cashew nuts, and apricots. This could make xylose a potential biomarker for the consumption of these foods. For example, although it looks and tastes exactly like ordinary sugar , having a 100% relative sweetness versus normal sucrose , it also has a low impact on blood sugar and insulin secretion and a minimal caloric value of 2.4 Calories/gm. In this pathway, xylose is first reduced to xylitol using the xylitol dehydrogenase (XDH) enzyme with NADH or NADPH. (d)-xylose is found in Allium chinense, Ascoseira mirabilis, Cajanus cajan, Cannabis sativa, Daucus carota, Daviesia latifolia, Diospyros kaki, Elliottia paniculata, Homo sapiens, Medicago lupulina, Aronia melanocarpa, Ramalina fraxinea, Saccharum officinarum, Tamarix aphylla, Tecoma stans, Vaccinium oxycoccos and Vachellia tortuosa. In particular, xylulose-5-phosphate can be used to directly generate glycerinaldehyde-3-phosphate in the pathway.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0326534 ((d)-xylose)


  Mrv1652305221919582D          

 13 12  0  0  1  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  2  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  9  1  1  0  0  0
  5 10  1  1  0  0  0
  3 11  1  1  0  0  0
  4 12  1  1  0  0  0
  5 13  1  1  0  0  0
M  END
Download

3D MOL for NP0326534 ((d)-xylose)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -3.3175    0.6887   -0.2286 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5930   -0.2406    0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2302   -0.0481    0.6052 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9918    1.3191    0.7276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1731   -0.6577   -0.3074 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1798   -0.1081   -1.5682 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1948   -0.6017    0.3425 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1823   -1.1602    1.6149 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7601    0.7896    0.3884 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7572    1.3212   -0.9105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9663   -1.2468   -0.1221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1990   -0.5627    1.5767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8827    1.7566    0.9028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4313   -1.7356   -0.4111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4522    0.8403   -1.5927 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9009   -1.2171   -0.2590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9969   -2.1205    1.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3070    1.4462    1.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8512    0.6749    0.6478 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4665    0.8624   -1.4373 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  7  5  1  0
  5  6  1  0
  5  3  1  0
  3  4  1  0
  3  2  1  0
  2  1  2  0
  7 16  1  6
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
  5 14  1  6
  6 15  1  0
  3 12  1  1
  4 13  1  0
  2 11  1  0
M  END
Download

3D SDF for NP0326534 ((d)-xylose)


  Mrv1652305221919582D          

 13 12  0  0  1  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  2  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  9  1  1  0  0  0
  5 10  1  1  0  0  0
  3 11  1  1  0  0  0
  4 12  1  1  0  0  0
  5 13  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0326534

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1

> <INCHI_KEY>
PYMYPHUHKUWMLA-VPENINKCSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.454511113538128

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-2.9380256209999995

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.420851692159264

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.332793333319174

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9744929158468105

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
31.3831

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xylose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0326534 ((d)-xylose)

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PDB for NP0326534 ((d)-xylose)
HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.025   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.976   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.691   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.357   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.644   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.358   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.976   3.644   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.691   3.644   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.357  -0.206   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0      -0.976   0.564   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.691   0.564   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.357   2.874   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    7                                                       
CONECT    3    1    5    8   11                                             
CONECT    4    2    5    9   12                                             
CONECT    5    3    4   10   13                                             
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0326534 ((d)-xylose)
Download
SMILES for NP0326534 ((d)-xylose)
[H][C@@](O)(CO)[C@]([H])(O)[C@@]([H])(O)C=O
Download
INCHI for NP0326534 ((d)-xylose)
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1
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View in JSmol
Synonyms
ValueSource
(+)-XyloseChEBI
(D)-XyloseChEBI
D-XylChEBI
D-XyloseChEBI
Wood sugarChEBI
D XyloseMeSH
XyloseMeSH
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2R,3S,4R)-2,3,4,5-tetrahydroxypentanal
Traditional Namexylose
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CO)[C@]([H])(O)[C@@]([H])(O)C=O
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1
InChI KeyPYMYPHUHKUWMLA-VPENINKCSA-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
Allium chinenseLOTUS Database
Ascoseira mirabilisLOTUS Database
Cajanus cajanLOTUS Database
Cannabis sativaLOTUS Database
Daucus carotaLOTUS Database
Daviesia latifoliaLOTUS Database
Diospyros kakiLOTUS Database
Elliottia paniculataLOTUS Database
Homo sapiensLOTUS Database
Medicago lupulinaLOTUS Database
Photinia melanocarpaLOTUS Database
Ramalina fraxineaLOTUS Database
Saccharum officinarumLOTUS Database
Tamarix aphyllaLOTUS Database
Tecoma stansLOTUS Database
Vaccinium oxycoccosLOTUS Database
Vachellia tortuosaLOTUS Database
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
    • 

  • Beta-hydroxy aldehyde
    • 

  • Alpha-hydroxyaldehyde
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Short-chain aldehyde
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-2.3ALOGPS
logP-2.9ChemAxon
logS0.4ALOGPS
pKa (Strongest Acidic)12.33ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.38 m³·mol⁻¹ChemAxon
Polarizability13.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB09419  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001136  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkXylose  
METLIN IDNot Available
PubChem Compound644160  
PDB IDNot Available
ChEBI ID15936  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]