Showing NP-Card for β-l-idopyranose (NP0281020)

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Record Information
Version2.0
Created at2022-09-09 07:07:28 UTC
Updated at2022-09-09 07:07:29 UTC
NP-MRD IDNP0281020
Secondary Accession NumbersNone
Natural Product Identification
Common Nameβ-l-idopyranose
DescriptionBeta-L-idopyranose, also known as beta-L-idose or β-L-idose, 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-l-idopyranose is found in Arabidopsis thaliana. β-l-idopyranose was first documented in 2004 (PMID: 14735509). Based on a literature review a small amount of articles have been published on beta-L-idopyranose (PMID: 14719939).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0281020 (β-l-idopyranose)

  Mrv1652309092209072D          

 12 12  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  1  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    0.8250    0.0000 C   0  0  2  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  6  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  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  1  6  0  0  0
M  END
Download

3D MOL for NP0281020 (β-l-idopyranose)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
    3.1224   -1.4478    0.1752 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5336   -0.2454   -0.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0952   -0.2169    0.2793 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4109   -1.2793   -0.3220 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8407   -1.4730    0.2589 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6283   -2.2118   -0.6207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5503   -0.1428    0.4750 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9110   -0.2440    0.3928 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9520    0.8145   -0.5436 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7041    1.9467   -0.7271 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4446    1.1156   -0.0103 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1779    1.8993   -0.8793 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4352   -2.0909    0.4803 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6077   -0.1316   -1.2871 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022    0.5724    0.3151 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0747   -0.4200    1.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7231   -2.0236    1.2177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5701   -2.1158   -0.3269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2730    0.1851    1.4993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3169    0.4388    1.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8153    0.2796   -1.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4088    2.3579   -1.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2750    1.6671    0.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4142    2.7660   -0.4289 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
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11  3  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  3 16  1  1
  5 17  1  1
  6 18  1  0
  7 19  1  1
  8 20  1  0
  9 21  1  6
 10 22  1  0
 11 23  1  1
 12 24  1  0
M  END
Download

3D SDF for NP0281020 (β-l-idopyranose)

  Mrv1652309092209072D          

 12 12  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   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 C   0  0  2  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
    0.0000    0.0000    0.0000 C   0  0  1  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    0.8250    0.0000 C   0  0  2  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  6  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  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
  3 11  1  0  0  0  0
 11 12  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0281020

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4-,5+,6-/m0/s1

> <INCHI_KEY>
WQZGKKKJIJFFOK-ZSNZIGRDSA-N

> <FORMULA>
C6H12O6

> <MOLECULAR_WEIGHT>
180.156

> <EXACT_MASS>
180.063388106

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.28336026316633

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6S)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol

> <JCHEM_LOGP>
-2.932539218

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.687538461190869

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.298101552080594

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810792051782764

> <JCHEM_POLAR_SURFACE_AREA>
110.38000000000001

> <JCHEM_REFRACTIVITY>
35.9234

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6S)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0281020 (β-l-idopyranose)

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PDB for NP0281020 (β-l-idopyranose)
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  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+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  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  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   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    3   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0281020 (β-l-idopyranose)
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SMILES for NP0281020 (β-l-idopyranose)
OC[C@@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
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INCHI for NP0281020 (β-l-idopyranose)
InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4-,5+,6-/m0/s1
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View in JSmol
Synonyms
ValueSource
beta-L-IdoseChEBI
WURCS=2.0/1,1,0/[a2121h-1b_1-5]/1/ChEBI
b-L-IdoseGenerator
Β-L-idoseGenerator
b-L-IdopyranoseGenerator
Β-L-idopyranoseGenerator
Chemical FormulaC6H12O6
Average Mass180.1560 Da
Monoisotopic Mass180.06339 Da
IUPAC Name(2S,3R,4S,5S,6S)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
Traditional Name(2S,3R,4S,5S,6S)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
CAS Registry NumberNot Available
SMILES
OC[C@@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4-,5+,6-/m0/s1
InChI KeyWQZGKKKJIJFFOK-ZSNZIGRDSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaLOTUS 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
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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-2.9ChemAxon
pKa (Strongest Acidic)11.3ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area110.38 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.92 m³·mol⁻¹ChemAxon
Polarizability16.28 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 ID4883375  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6323336  
PDB IDNot Available
ChEBI ID72452  
Good Scents IDNot Available
References
General References
  1. Lee JC, Chang SW, Liao CC, Chi FC, Chen CS, Wen YS, Wang CC, Kulkarni SS, Puranik R, Liu YH, Hung SC: From D-glucose to biologically potent L-hexose derivatives: synthesis of alpha-L-iduronidase fluorogenic detector and the disaccharide moieties of bleomycin A2 and heparan sulfate. Chemistry. 2004 Jan 23;10(2):399-415. doi: 10.1002/chem.200305096. [PubMed:14735509  ] 
  2. Lee JC, Lu XA, Kulkarni SS, Wen YS, Hung SC: Synthesis of heparin oligosaccharides. J Am Chem Soc. 2004 Jan 21;126(2):476-7. doi: 10.1021/ja038244h. [PubMed:14719939  ] 
  3. LOTUS database [Link]