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Showing NP-Card for (2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol (NP0268510)

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Record Information
Version2.0
Created at2022-09-08 13:39:32 UTC
Updated at2022-09-08 13:39:32 UTC
NP-MRD IDNP0268510
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol
Description1-Deoxy-d-glucitol 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. (2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol is found in Anethum graveolens, Carum carvi, Cnidium monnieri, Foeniculum vulgare and Trachyspermum ammi. (2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol was first documented in 2004 (PMID: 15063204). Based on a literature review a small amount of articles have been published on 1-deoxy-d-glucitol (PMID: 24685455) (PMID: 20423159) (PMID: 20382375) (PMID: 16519455).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)


  Mrv1652309082215392D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  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  2  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  1  0  0  0  0
  2  3  1  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  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 NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
    2.7637   -0.4887    0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9066    0.6908   -0.2588 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6009    1.8521    0.0178 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5636    0.6546    0.4622 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1585    1.7576    0.0122 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1124   -0.6197    0.0594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2095   -0.6733   -1.3371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4742   -0.8260    0.6335 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9131   -2.1006    0.1992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5070    0.1499    0.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6188    0.1216   -1.2146 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7977   -0.2678   -0.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8418   -0.5799    1.2404 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4181   -1.4428   -0.3231 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7493    0.6572   -1.3557 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0516    2.6515   -0.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6905    0.7498    1.5531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1694    1.7716   -0.9765 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5065   -1.4985    0.4137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2884   -1.6059   -1.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4705   -0.8176    1.7438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1030   -2.0226   -0.7753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912   -0.1941    0.5753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3287    1.1587    0.5885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0457    0.9221   -1.5763 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  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
  2 15  1  6
  3 16  1  0
  4 17  1  1
  5 18  1  0
  6 19  1  1
  7 20  1  0
  8 21  1  1
  9 22  1  0
 10 23  1  0
 10 24  1  0
 11 25  1  0
M  END
Download

3D SDF for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)


  Mrv1652309082215392D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  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  2  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  1  0  0  0  0
  2  3  1  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  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>
NP0268510

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O5/c1-3(8)5(10)6(11)4(9)2-7/h3-11H,2H2,1H3/t3-,4+,5+,6+/m0/s1

> <INCHI_KEY>
SKCKOFZKJLZSFA-SLPGGIOYSA-N

> <FORMULA>
C6H14O5

> <MOLECULAR_WEIGHT>
166.173

> <EXACT_MASS>
166.084123551

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.162239464796418

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5S)-hexane-1,2,3,4,5-pentol

> <JCHEM_LOGP>
-2.683108882

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.642051755496475

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.69525446645461

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742106409022417

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
36.859899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5S)-hexane-1,2,3,4,5-pentol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)

Download
PDB for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)
HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    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 NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)
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SMILES for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)
C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
Download
INCHI for NP0268510 ((2r,3r,4r,5s)-hexane-1,2,3,4,5-pentol)
InChI=1S/C6H14O5/c1-3(8)5(10)6(11)4(9)2-7/h3-11H,2H2,1H3/t3-,4+,5+,6+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H14O5
Average Mass166.1730 Da
Monoisotopic Mass166.08412 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C6H14O5/c1-3(8)5(10)6(11)4(9)2-7/h3-11H,2H2,1H3/t3-,4+,5+,6+/m0/s1
InChI KeySKCKOFZKJLZSFA-SLPGGIOYSA-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
Anethum graveolensLOTUS Database
Carum carviLOTUS Database
Cnidium monnieriLOTUS Database
Foeniculum vulgareLOTUS Database
Trachyspermum ammiLOTUS 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
    • 

  • Fatty alcohol
    • 

  • Fatty acyl
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00036426  
Chemspider ID8853977  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10678630  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Slusarz R, Szulc M, Madaj J: Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties. Carbohydr Res. 2014 May 7;389:154-64. doi: 10.1016/j.carres.2014.02.002. Epub  2014 Feb 12. [PubMed:24685455  ] 
  2. Vlahov IR, Santhapuram HK, You F, Wang Y, Kleindl PJ, Hahn SJ, Vaughn JF, Reno DS, Leamon CP: Carbohydrate-based synthetic approach to control toxicity profiles of folate-drug conjugates. J Org Chem. 2010 Jun 4;75(11):3685-91. doi: 10.1021/jo100448q. [PubMed:20423159  ] 
  3. Kaplanek R, Polak R, Paleta O, Kefurt K, Moravcova J, Krenova I, Kodicek M: Perfluoroalkylated derivatives of 6-deoxy-6-ethylamino-D-galactose, 1-deoxy-1-methylamino-D-glucitol, and 1-amino-1-deoxy-D-glucitol: syntheses, hemocompatibility, and effect on perfluorocarbon emulsion. Carbohydr Res. 2010 May 27;345(8):1008-14. doi: 10.1016/j.carres.2010.03.023.  Epub 2010 Mar 27. [PubMed:20382375  ] 
  4. Scarzello M, Klijn JE, Wagenaar A, Stuart MC, Hulst R, Engberts JB: pH-Dependent aggregation properties of mixtures of sugar-based gemini surfactants with phospholipids and single-tailed surfactants. Langmuir. 2006 Mar 14;22(6):2558-68. doi: 10.1021/la053211w. [PubMed:16519455  ] 
  5. Schuur B, Wagenaar A, Heeres A, Heeres EH: A synthetic strategy for novel nonsymmetrical bola amphiphiles based on carbohydrates. Carbohydr Res. 2004 Apr 28;339(6):1147-53. doi: 10.1016/j.carres.2004.01.021. [PubMed:15063204  ] 
  6. LOTUS database [Link]