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Showing NP-Card for (2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one (NP0304877)

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Record Information
Version2.0
Created at2022-09-10 20:16:16 UTC
Updated at2022-09-10 20:16:16 UTC
NP-MRD IDNP0304877
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one
DescriptionGabosine B 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. (2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one was first documented in 2019 (PMID: 30951069). Based on a literature review very few articles have been published on Gabosine B.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)


  Mrv1652309102222162D          

 11 11  0  0  1  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  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  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
    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 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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  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
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
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3D MOL for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)

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3D SDF for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)

  Mrv1652309102222162D          

 11 11  0  0  1  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  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  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
    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 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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  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
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0304877

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@@H](O)[C@@H](O)[C@H](O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O4/c1-3-2-4(8)6(10)7(11)5(3)9/h3-4,6-8,10-11H,2H2,1H3/t3-,4-,6-,7-/m1/s1

> <INCHI_KEY>
FQFXYFNHFVFHPV-PFFCINGUSA-N

> <FORMULA>
C7H12O4

> <MOLECULAR_WEIGHT>
160.169

> <EXACT_MASS>
160.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.36739384526763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,6R)-2,3,4-trihydroxy-6-methylcyclohexan-1-one

> <JCHEM_LOGP>
-0.9896925916666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.834297131741682

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.099453161492274

> <JCHEM_PKA_STRONGEST_BASIC>
-3.199158772572005

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
37.0371

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,6R)-2,3,4-trihydroxy-6-methylcyclohexan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)
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PDB for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)
HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+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  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -2.310   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  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+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   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    2   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 NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)
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SMILES for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)
C[C@@H]1C[C@@H](O)[C@@H](O)[C@H](O)C1=O
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INCHI for NP0304877 ((2s,3r,4r,6r)-2,3,4-trihydroxy-6-methylcyclohexan-1-one)
InChI=1S/C7H12O4/c1-3-2-4(8)6(10)7(11)5(3)9/h3-4,6-8,10-11H,2H2,1H3/t3-,4-,6-,7-/m1/s1
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SynonymsNot Available
Chemical FormulaC7H12O4
Average Mass160.1690 Da
Monoisotopic Mass160.07356 Da
IUPAC Name(2S,3R,4R,6R)-2,3,4-trihydroxy-6-methylcyclohexan-1-one
Traditional Name(2S,3R,4R,6R)-2,3,4-trihydroxy-6-methylcyclohexan-1-one
CAS Registry NumberNot Available
SMILES
C[C@@H]1C[C@@H](O)[C@@H](O)[C@H](O)C1=O
InChI Identifier
InChI=1S/C7H12O4/c1-3-2-4(8)6(10)7(11)5(3)9/h3-4,6-8,10-11H,2H2,1H3/t3-,4-,6-,7-/m1/s1
InChI KeyFQFXYFNHFVFHPV-PFFCINGUSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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
    • 

  • Cyclic ketone
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • 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
logP-0.99ChemAxon
pKa (Strongest Acidic)12.1ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.04 m³·mol⁻¹ChemAxon
Polarizability15.37 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 ID10389084  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21768265  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yang X, Yuan P, Shui F, Zhou Y, Chen X: A divergent strategy to synthesize gabosines featuring a switchable two-way aldol cyclization. Org Biomol Chem. 2019 Apr 17;17(16):4061-4072. doi: 10.1039/c9ob00469f. [PubMed:30951069  ] 
  2. LOTUS database [Link]