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Showing NP-Card for xylosone (NP0322126)

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Record Information
Version2.0
Created at2022-09-12 00:43:27 UTC
Updated at2022-09-12 00:43:27 UTC
NP-MRD IDNP0322126
Secondary Accession NumbersNone
Natural Product Identification
Common Namexylosone
Description2-Keto-D-xylose, also known as D-xylosone, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. xylosone is found in Brevundimonas diminuta. xylosone was first documented in 1993 (PMID: 8319689). Based on a literature review very few articles have been published on 2-keto-D-xylose (PMID: 11086703).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0322126 (xylosone)


  Mrv1652309122202432D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0322126 (xylosone)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2774   -1.7711    1.5822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0307   -0.9531    1.0116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6481   -0.3636   -0.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5036    0.4001   -0.7827 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3830   -0.5528   -0.9590 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6229   -0.2419   -2.3171 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6558    0.4110   -0.4216 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8600    0.2849   -1.1221 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8539    0.3108    1.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7563    1.3247    1.5011 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9611   -0.7197    1.4995 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0099   -1.5798   -0.9455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1901   -0.3532   -2.8571 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3129    1.4668   -0.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1289   -0.6521   -1.2434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0952    0.5982    1.5617 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1932   -0.6718    1.4059 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5610    0.9154    1.8966 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  7  1  0
  7  8  1  0
  7  5  1  0
  5  6  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  2  0
 10 18  1  0
  9 16  1  0
  9 17  1  0
  7 14  1  1
  8 15  1  0
  5 12  1  6
  6 13  1  0
  2 11  1  0
M  END
Download

3D SDF for NP0322126 (xylosone)


  Mrv1652309122202432D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0322126

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-1-3(8)5(10)4(9)2-7/h1,4-5,7,9-10H,2H2/t4-,5-/m1/s1

> <INCHI_KEY>
VDSAQEDKJUSZPS-RFZPGFLSSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173358

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.868405105231211

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.729778228

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.171157702863212

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.711436437485396

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9800510738495127

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
30.753399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
xylosone

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0322126 (xylosone)

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PDB for NP0322126 (xylosone)
HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0322126 (xylosone)
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SMILES for NP0322126 (xylosone)
OC[C@@H](O)[C@H](O)C(=O)C=O
Download
INCHI for NP0322126 (xylosone)
InChI=1S/C5H8O5/c6-1-3(8)5(10)4(9)2-7/h1,4-5,7,9-10H,2H2/t4-,5-/m1/s1
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View in JSmol
Synonyms
ValueSource
(3S,4R)-3,4,5-Trihydroxy-2-oxopentanalChEBI
2-Dehydro-D-xyloseChEBI
D-LyxosoneChEBI
D-XylosoneChEBI
Threo-pentos-2-uloseChEBI
XylosoneMeSH
Threo-pentos-2-ulose, (D)-isomerMeSH
Chemical FormulaC5H8O5
Average Mass148.1140 Da
Monoisotopic Mass148.03717 Da
IUPAC Name(3S,4R)-3,4,5-trihydroxy-2-oxopentanal
Traditional Namexylosone
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@H](O)C(=O)C=O
InChI Identifier
InChI=1S/C5H8O5/c6-1-3(8)5(10)4(9)2-7/h1,4-5,7,9-10H,2H2/t4-,5-/m1/s1
InChI KeyVDSAQEDKJUSZPS-RFZPGFLSSA-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
Brevundimonas diminutaLOTUS 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
    • 

  • Acyloin
    • 

  • Beta-hydroxy aldehyde
    • 

  • Beta-hydroxy ketone
    • 

  • Alpha-ketoaldehyde
    • 

  • Alpha-hydroxy ketone
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Primary alcohol
    • 

  • Short-chain aldehyde
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.7ChemAxon
pKa (Strongest Acidic)9.71ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.75 m³·mol⁻¹ChemAxon
Polarizability12.87 ųChemAxon
Number of Rings0ChemAxon
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 ID140750  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound160122  
PDB IDNot Available
ChEBI ID46675  
Good Scents IDNot Available
References
General References
  1. Volc J, Sedmera P, Halada P, Prikrylova V, Haltrich D: Double oxidation of D-xylose to D-glycero -pentos-2,3-diulose (2,3-diketo-D-xylose) by pyranose dehydrogenase from the mushroom Agaricus bisporus. Carbohydr Res. 2000 Oct 20;329(1):219-25. doi: 10.1016/s0008-6215(00)00167-1. [PubMed:11086703  ] 
  2. Danneel HJ, Rossner E, Zeeck A, Giffhorn F: Purification and characterization of a pyranose oxidase from the basidiomycete Peniophora gigantea and chemical analyses of its reaction products. Eur J Biochem. 1993 Jun 15;214(3):795-802. doi: 10.1111/j.1432-1033.1993.tb17982.x. [PubMed:8319689  ] 
  3. LOTUS database [Link]