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Showing NP-Card for vibo-Quercitol (NP0140272)

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Record Information
Version2.0
Created at2022-06-29 21:20:47 UTC
Updated at2022-06-29 21:20:47 UTC
NP-MRD IDNP0140272
Secondary Accession NumbersNone
Natural Product Identification
Common Namevibo-Quercitol
DescriptionVibo-Quercitol belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring. vibo-Quercitol is found in Diploclisia glaucescens and Marsdenia tomentosa. vibo-Quercitol was first documented in 2017 (PMID: 28905086). Based on a literature review a small amount of articles have been published on vibo-Quercitol (PMID: 32670790) (PMID: 31237686) (PMID: 29663050) (PMID: 29183694).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0140272 (vibo-Quercitol)


  Mrv1652306292223202D          

 11 11  0  0  1  0            999 V2000
    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
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   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 C   0  0  2  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 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
    0.7145   -1.2375    0.0000 O   0  0  0  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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  1  0  0  0
  4  9  1  0  0  0  0
  3 10  1  1  0  0  0
  2 11  1  1  0  0  0
M  END
Download

3D MOL for NP0140272 (vibo-Quercitol)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
    0.4808   -1.5735    1.6097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0774   -1.4958    0.3563 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8418   -0.8716   -0.6687 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0466   -1.5262   -0.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0961    0.5790   -0.3236 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7301    0.6983    0.9190 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1662    1.3906   -0.3031 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1494    2.6445    0.2182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1668    0.7473    0.6251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3734   -0.7170    0.3305 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8594   -0.7972   -0.9871 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2770   -0.7207    2.0781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3029   -2.5223    0.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2846   -0.8713   -1.6350 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0889   -1.9430   -1.6961 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7880    0.9995   -1.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5677    0.1755    0.9482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5684    1.4595   -1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2064    3.3894   -0.3301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1529    1.2434    0.4805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8482    0.9335    1.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0951   -1.1031    1.0651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5339   -0.1188   -1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  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  1  0
  3  2  1  0
  2  1  1  0
  2 10  1  0
 11 23  1  0
 10 22  1  1
  9 20  1  0
  9 21  1  0
  7 18  1  6
  8 19  1  0
  5 16  1  6
  6 17  1  0
  3 14  1  6
  4 15  1  0
  2 13  1  6
  1 12  1  0
M  END
Download

3D SDF for NP0140272 (vibo-Quercitol)


  Mrv1652306292223202D          

 11 11  0  0  1  0            999 V2000
    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
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   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 C   0  0  2  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 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
    0.7145   -1.2375    0.0000 O   0  0  0  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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  1  0  0  0
  4  9  1  0  0  0  0
  3 10  1  1  0  0  0
  2 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0140272

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c7-2-1-3(8)5(10)6(11)4(2)9/h2-11H,1H2/t2-,3-,4-,5+,6?/m1/s1

> <INCHI_KEY>
IMPKVMRTXBRHRB-RSVSWTKNSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.218886337591352

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.55

> <JCHEM_LOGP>
-3.091714970999999

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.453973124049774

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.609915603511627

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2214237570389086

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
34.677899999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e+03 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0140272 (vibo-Quercitol)

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PDB for NP0140272 (vibo-Quercitol)
HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   11                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    4                                                            
CONECT   10    3                                                            
CONECT   11    2                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0140272 (vibo-Quercitol)
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SMILES for NP0140272 (vibo-Quercitol)
O[C@@H]1C[C@@H](O)[C@@H](O)C(O)[C@H]1O
Download
INCHI for NP0140272 (vibo-Quercitol)
InChI=1S/C6H12O5/c7-2-1-3(8)5(10)6(11)4(2)9/h2-11H,1H2/t2-,3-,4-,5+,6?/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
O[C@@H]1C[C@@H](O)[C@@H](O)C(O)[C@H]1O
InChI Identifier
InChI=1S/C6H12O5/c7-2-1-3(8)5(10)6(11)4(2)9/h2-11H,1H2/t2-,3-,4-,5+,6?/m1/s1
InChI KeyIMPKVMRTXBRHRB-RSVSWTKNSA-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
Diploclisia glaucescensLOTUS Database
Marsdenia tomentosaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentCyclohexanols  
Alternative Parents
Substituents
  • Cyclohexanol
    • 

  • Cyclitol or derivatives
    • 

  • Cyclic alcohol
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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 IDNot Available
Chemspider ID390171  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound441438  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Al-Fahad AJ, Al-Fageeh MB, Kharbatia NM, Sioud S, Mahadevan R: Metabolically engineered recombinant Saccharomyces cerevisiae for the production of 2-Deoxy-scyllo-inosose (2-DOI). Metab Eng Commun. 2020 May 31;11:e00134. doi: 10.1016/j.mec.2020.e00134. eCollection 2020 Dec. [PubMed:32670790  ] 
  2. Bai X, Meng D, Wei X, Zhou X, Lu F, You C: Facile synthesis of (-)-vibo-quercitol from maltodextrin via an in vitro synthetic enzymatic biosystem. Biotechnol Bioeng. 2019 Oct;116(10):2710-2719. doi: 10.1002/bit.27096. Epub 2019  Jul 12. [PubMed:31237686  ] 
  3. Itoh N: Biosynthesis and production of quercitols and their application in the production of pharmaceuticals: current status and prospects. Appl Microbiol Biotechnol. 2018 Jun;102(11):4641-4651. doi:  10.1007/s00253-018-8972-y. Epub 2018 Apr 17. [PubMed:29663050  ] 
  4. Ara S, Yamazaki H, Takaku H: Isolation of 2-deoxy-scyllo-inosose (DOI)-assimilating yeasts and cloning and characterization of the DOI reductase gene of Cryptococcus podzolicus ND1. J Biosci Bioeng. 2018 Apr;125(4):397-406. doi: 10.1016/j.jbiosc.2017.10.019. Epub  2017 Nov 26. [PubMed:29183694  ] 
  5. Itoh N, Kurokawa J, Toda H, Konishi K: Identification and characterization of a novel (-)-vibo-quercitol 1-dehydrogenase from Burkholderia terrae suitable for production of (-)-vibo-quercitol from 2-deoxy-scyllo-inosose. Appl Microbiol Biotechnol. 2017 Oct;101(20):7545-7555. doi:  10.1007/s00253-017-8483-2. Epub 2017 Sep 13. [PubMed:28905086  ]