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Showing NP-Card for β-cymaropyranose (NP0289560)

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Record Information
Version2.0
Created at2022-09-09 19:48:52 UTC
Updated at2022-09-09 19:48:52 UTC
NP-MRD IDNP0289560
Secondary Accession NumbersNone
Natural Product Identification
Common Nameβ-cymaropyranose
DescriptionBeta-Cymaropyranose, also known as D-cymarose, belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity. β-cymaropyranose is found in Cynanchum wilfordii, Hoodia gordonii and Hoya carnosa. Based on a literature review very few articles have been published on beta-Cymaropyranose.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0289560 (β-cymaropyranose)


  Mrv1652309092221482D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    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  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  1  0  0  0
M  END
Download

3D MOL for NP0289560 (β-cymaropyranose)

     RDKit          3D

 25 25  0  0  0  0  0  0  0  0999 V2000
    2.4114   -1.5888   -0.5385 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2185   -0.8749   -0.7295 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9661   -0.0173    0.3288 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8768    1.3903   -0.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4276    1.7391   -0.8097 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5880    3.1333   -0.7987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5351    1.2034   -0.1768 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4077   -0.1978   -0.0817 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7079   -0.8660    0.2011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3498   -0.4385    0.9569 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2974   -1.7253    1.4241 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5528   -2.2503   -1.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3601   -2.1431    0.4067 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2427   -0.8516   -0.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7751   -0.0951    1.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1223    2.0872    0.6238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6710    1.5031   -0.9617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4666    1.4308   -1.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2866    3.6030   -0.7903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0132   -0.5255   -1.0641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9143   -1.0378    1.2696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5184   -0.2279   -0.2536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7745   -1.8536   -0.3063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5145    0.2781    1.8101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0317   -1.6749    2.3773 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  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  3  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  5 18  1  6
  6 19  1  0
  8 20  1  6
  9 21  1  0
  9 22  1  0
  9 23  1  0
 10 24  1  1
 11 25  1  0
M  END
Download

3D SDF for NP0289560 (β-cymaropyranose)


  Mrv1652309092221482D          

 11 11  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    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  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0289560

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H14O4/c1-4-7(9)5(10-2)3-6(8)11-4/h4-9H,3H2,1-2H3/t4-,5+,6-,7-/m1/s1

> <INCHI_KEY>
DBDJCJKVEBFXHG-XZBKPIIZSA-N

> <FORMULA>
C7H14O4

> <MOLECULAR_WEIGHT>
162.185

> <EXACT_MASS>
162.089208931

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.300411714958862

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4S,5R,6R)-4-methoxy-6-methyloxane-2,5-diol

> <JCHEM_LOGP>
-0.34186468466666703

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.288687473203698

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.318126399418777

> <JCHEM_PKA_STRONGEST_BASIC>
-3.579485317318233

> <JCHEM_POLAR_SURFACE_AREA>
58.92

> <JCHEM_REFRACTIVITY>
37.6202

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
β-cymaropyranose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0289560 (β-cymaropyranose)

Download
PDB for NP0289560 (β-cymaropyranose)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    3   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0289560 (β-cymaropyranose)
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SMILES for NP0289560 (β-cymaropyranose)
CO[C@H]1C[C@H](O)O[C@H](C)[C@H]1O
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INCHI for NP0289560 (β-cymaropyranose)
InChI=1S/C7H14O4/c1-4-7(9)5(10-2)3-6(8)11-4/h4-9H,3H2,1-2H3/t4-,5+,6-,7-/m1/s1
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View in JSmol
Synonyms
ValueSource
D-CymaroseKegg
CymaroseKegg
2,6-Dideoxy-3-O-methyl-D-ribo-hexoseKegg
b-CymaropyranoseGenerator
Β-cymaropyranoseGenerator
Chemical FormulaC7H14O4
Average Mass162.1850 Da
Monoisotopic Mass162.08921 Da
IUPAC Name(2R,4S,5R,6R)-4-methoxy-6-methyloxane-2,5-diol
Traditional Nameβ-cymaropyranose
CAS Registry NumberNot Available
SMILES
CO[C@H]1C[C@H](O)O[C@H](C)[C@H]1O
InChI Identifier
InChI=1S/C7H14O4/c1-4-7(9)5(10-2)3-6(8)11-4/h4-9H,3H2,1-2H3/t4-,5+,6-,7-/m1/s1
InChI KeyDBDJCJKVEBFXHG-XZBKPIIZSA-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
Cynanchum wilfordiiLOTUS Database
Hoodia gordoniiLOTUS Database
Hoya carnosaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentHexoses  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • 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-0.34ChemAxon
pKa (Strongest Acidic)12.32ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.62 m³·mol⁻¹ChemAxon
Polarizability16.3 ųChemAxon
Number of Rings1ChemAxon
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 ID390151  
KEGG Compound IDC08234  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound441417  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]