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Showing NP-Card for 2-o-methylxylose (NP0220844)

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Record Information
Version2.0
Created at2022-09-05 22:16:01 UTC
Updated at2022-09-05 22:16:01 UTC
NP-MRD IDNP0220844
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-o-methylxylose
Description2-O-methylxylose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 2-o-methylxylose is found in Medicago sativa. 2-o-methylxylose was first documented in 2005 (PMID: 15963960). Based on a literature review very few articles have been published on 2-o-methylxylose.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0220844 (2-o-methylxylose)


  Mrv1652309062200162D          

 11 10  0  0  1  0            999 V2000
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for NP0220844 (2-o-methylxylose)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
    3.0908   -0.3916   -0.5110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1676    0.6215   -0.7245 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1170    0.5777    0.1943 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0053    1.8060    0.9777 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1870    1.9839    1.8532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1793    0.2760   -0.5526 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0429   -0.9749   -1.2171 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3293    0.1206    0.3870 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9993   -0.9049    1.2887 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5236   -0.4096   -0.3979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5924   -0.6940    0.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5662   -0.3776    0.4660 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8013   -0.3842   -1.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5098   -1.3550   -0.5817 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2990   -0.2780    0.8732 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7015    2.6287    0.7701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3423    1.0187   -1.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1085   -1.6709   -0.5063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6538    1.0259    0.8976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4314   -0.6849    2.1479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1789   -1.3361   -0.9169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7873    0.3455   -1.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2764   -0.9426    1.3132 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  2  0
  3  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  1
  4 16  1  0
  6 17  1  6
  7 18  1  0
  8 19  1  1
  9 20  1  0
 10 21  1  0
 10 22  1  0
 11 23  1  0
M  END
Download

3D SDF for NP0220844 (2-o-methylxylose)


  Mrv1652309062200162D          

 11 10  0  0  1  0            999 V2000
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0220844

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-11-5(3-8)6(10)4(9)2-7/h3-7,9-10H,2H2,1H3/t4-,5+,6+/m1/s1

> <INCHI_KEY>
ALNDFFUAQIVVPG-SRQIZXRXSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.582035818477351

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.294899117333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.209984726479338

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.815144399847664

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9744989154276755

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
36.134299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R)-3,4,5-trihydroxy-2-methoxypentanal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0220844 (2-o-methylxylose)

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PDB for NP0220844 (2-o-methylxylose)
HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.390   1.334   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.930  -1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.700  -2.667   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.700   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.930   1.334   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.240   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.010   1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0220844 (2-o-methylxylose)
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SMILES for NP0220844 (2-o-methylxylose)
CO[C@@H](C=O)[C@@H](O)[C@H](O)CO
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INCHI for NP0220844 (2-o-methylxylose)
InChI=1S/C6H12O5/c1-11-5(3-8)6(10)4(9)2-7/h3-7,9-10H,2H2,1H3/t4-,5+,6+/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC Name(2R,3S,4R)-3,4,5-trihydroxy-2-methoxypentanal
Traditional Name(2R,3S,4R)-3,4,5-trihydroxy-2-methoxypentanal
CAS Registry NumberNot Available
SMILES
CO[C@@H](C=O)[C@@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C6H12O5/c1-11-5(3-8)6(10)4(9)2-7/h3-7,9-10H,2H2,1H3/t4-,5+,6+/m1/s1
InChI KeyALNDFFUAQIVVPG-SRQIZXRXSA-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
Medicago sativaLOTUS 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
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Polyol
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-2.3ChemAxon
pKa (Strongest Acidic)12.82ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.13 m³·mol⁻¹ChemAxon
Polarizability15.58 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 ID20041587  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14536300  
PDB IDNot Available
ChEBI ID173727  
Good Scents IDNot Available
References
General References
  1. Sassaki GL, Gorin PA, Reis RA, Serrato RV, Elifio SL, Iacomini M: Carbohydrate, glycolipid, and lipid components from the photobiont (Scytonema sp.) of the lichen, Dictyomema glabratum. Carbohydr Res. 2005 Aug 15;340(11):1808-17. doi: 10.1016/j.carres.2005.05.004. [PubMed:15963960  ] 
  2. LOTUS database [Link]