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Showing NP-Card for conduritol (NP0267985)

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Record Information
Version2.0
Created at2022-09-08 12:57:20 UTC
Updated at2022-09-08 12:57:20 UTC
NP-MRD IDNP0267985
Secondary Accession NumbersNone
Natural Product Identification
Common Nameconduritol
DescriptionConduritol belongs to the class of organic compounds known as cyclitols and derivatives. Cyclitols and derivatives are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms. These of also include derivatives where the hydrogen atom of one or more of the hydroxyl groups is replaced with another atom. conduritol is found in Dregea volubilis, Gymnema sylvestre and Leptadenia arborea. conduritol was first documented in 2002 (PMID: 12003543). Conduritol is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 16267592) (PMID: 21630704).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0267985 (conduritol)


  Mrv1533004161504452D          

 10 10  0  0  0  0            999 V2000
    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  0  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  0  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
    0.7145   -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  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    0.8250    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0267985 (conduritol)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    0.1784   -1.3866   -1.2012 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4875   -1.0228    0.1173 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5331    0.0440    0.0583 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8299    0.5441    1.3254 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9983    1.1579   -0.7717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2732    1.4907   -0.5454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1524    0.8534    0.4348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4691    0.9345   -0.0158 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7896   -0.5589    0.7690 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8115   -1.4100    0.3481 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7618   -2.1359   -1.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8394   -1.9407    0.6368 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4261   -0.3735   -0.4364 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5259    0.0241    1.7950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6276    1.6355   -1.4939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7066    2.3149   -1.1417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1214    1.4424    1.3937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4977    0.6983   -0.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6749   -0.7202    1.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7118   -1.5913   -0.6355 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  2  1  1  0
  2  3  1  0
  4 14  1  0
  3 13  1  6
  5 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
  2 12  1  1
  1 11  1  0
M  END
Download

3D SDF for NP0267985 (conduritol)


  Mrv1533004161504452D          

 10 10  0  0  0  0            999 V2000
    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  0  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  0  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
    0.7145   -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  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    0.8250    0.0000 C   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0267985

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C=CC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c7-3-1-2-4(8)6(10)5(3)9/h1-10H

> <INCHI_KEY>
LRUBQXAKGXQBHA-UHFFFAOYSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.142

> <EXACT_MASS>
146.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.365826730910687

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclohex-5-ene-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-1.9941240946666667

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.68564452444308

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.696148840327574

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3494846981628417

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
34.1686

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.89e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
conduritol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0267985 (conduritol)

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PDB for NP0267985 (conduritol)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0267985 (conduritol)
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SMILES for NP0267985 (conduritol)
OC1C=CC(O)C(O)C1O
Download
INCHI for NP0267985 (conduritol)
InChI=1S/C6H10O4/c7-3-1-2-4(8)6(10)5(3)9/h1-10H
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View in JSmol
Synonyms
ValueSource
Conduritol CMeSH
Conduritol b, (1R-(1alpha,2alpha,3beta,4alpha))-isomerMeSH
5-Cyclohexene-1,2,3,4-tetrolMeSH
Conduritol b, (1alpha,2alpha,3alpha,4beta)-isomerMeSH
Conduritol aMeSH
Conduritol b, (1alpha,2beta,3beta,4alpha)-isomerMeSH
Conduritol bMeSH
Chemical FormulaC6H10O4
Average Mass146.1420 Da
Monoisotopic Mass146.05791 Da
IUPAC Namecyclohex-5-ene-1,2,3,4-tetrol
Traditional Nameconduritol
CAS Registry NumberNot Available
SMILES
OC1C=CC(O)C(O)C1O
InChI Identifier
InChI=1S/C6H10O4/c7-3-1-2-4(8)6(10)5(3)9/h1-10H
InChI KeyLRUBQXAKGXQBHA-UHFFFAOYSA-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
Dregea volubilisLOTUS Database
Gymnema sylvestreLOTUS Database
Leptadenia arboreaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclitols and derivatives. Cyclitols and derivatives are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms. These of also include derivatives where the hydrogen atom of one or more of the hydroxyl groups is replaced with another atom.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentCyclitols and derivatives  
Alternative Parents
Substituents
  • Cyclitol or derivatives
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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-2.3ALOGPS
logP-2ChemAxon
logS0.42ALOGPS
pKa (Strongest Acidic)12.7ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity34.17 m³·mol⁻¹ChemAxon
Polarizability13.37 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkConduritol  
METLIN IDNot Available
PubChem Compound136345  
PDB IDNot Available
ChEBI ID67218  
Good Scents IDNot Available
References
General References
  1. Kwon YU, Lee C, Chung SK: Facile syntheses of all possible diastereomers of conduritol and various derivatives of inositol stereoisomers in high enantiopurity from myo-inositol. J Org Chem. 2002 May 17;67(10):3327-38. doi: 10.1021/jo016237a. [PubMed:12003543  ] 
  2. Keinicke L, Madsen R: A concise synthetic route to the conduritols from pentoses. Org Biomol Chem. 2005 Nov 21;3(22):4124-8. doi: 10.1039/b512009h. Epub 2005 Oct 4. [PubMed:16267592  ] 
  3. Duchek J, Adams DR, Hudlicky T: Chemoenzymatic synthesis of inositols, conduritols, and cyclitol analogues. Chem Rev. 2011 Jul 13;111(7):4223-58. doi: 10.1021/cr1004138. Epub 2011 Jun 1. [PubMed:21630704  ] 
  4. LOTUS database [Link]