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Showing NP-Card for (3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one (NP0314202)

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Record Information
Version2.0
Created at2022-09-11 12:10:57 UTC
Updated at2022-09-11 12:10:58 UTC
NP-MRD IDNP0314202
Secondary Accession NumbersNone
Natural Product Identification
Common Name(3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one
DescriptionSCHEMBL14031511 belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. (3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one is found in Streptomyces albidoflavus. Based on a literature review very few articles have been published on SCHEMBL14031511.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)


  Mrv1652309112214102D          

 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  1  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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    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 C   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 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 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  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  1  6  0  0  0
M  END
Download

3D MOL for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)

     RDKit          3D

 25 25  0  0  0  0  0  0  0  0999 V2000
    2.8135   -0.0473   -0.2506 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3666    0.1497    0.0461 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9085    1.5481   -0.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7068    2.5003    0.0428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3975    1.7954   -0.3988 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4247    0.8357   -0.4404 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4062    1.1686    0.6708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9241   -0.5764   -0.3329 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0037   -1.1265    1.0666 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4820   -0.6894   -0.8675 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8992   -1.9989   -0.7609 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2803    0.8470   -0.7077 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3950   -0.4048    0.6488 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9183   -0.8887   -0.9893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1922   -0.1305    1.1178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9353    0.9379   -1.4201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0696    1.9704    0.2856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9962    0.2969    0.9873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8614    1.6396    1.5389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5529   -1.2563   -0.9755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0865   -1.7066    1.3522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1222   -0.3441    1.8295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8467   -1.8544    1.1834 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5414   -0.2721   -1.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1233   -2.3936   -1.6401 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  1  0
  2 10  1  0
 10 11  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  7 17  1  0
  7 18  1  0
  7 19  1  0
  6 16  1  6
  2 15  1  1
  1 12  1  0
  1 13  1  0
  1 14  1  0
 10 24  1  6
 11 25  1  0
  8 20  1  6
  9 21  1  0
  9 22  1  0
  9 23  1  0
M  END
Download

3D SDF for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)


  Mrv1652309112214102D          

 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  1  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
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    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 C   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 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 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  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  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0314202

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O3/c1-4-6(3)11-8(10)5(2)7(4)9/h4-7,9H,1-3H3/t4-,5+,6+,7-/m0/s1

> <INCHI_KEY>
WIPAYFJRYZXVMZ-WNJXEPBRSA-N

> <FORMULA>
C8H14O3

> <MOLECULAR_WEIGHT>
158.197

> <EXACT_MASS>
158.094294311

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.612058004323316

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R,6R)-4-hydroxy-3,5,6-trimethyloxan-2-one

> <JCHEM_LOGP>
0.7293997600000004

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.372498955968041

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0732689566595788

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
39.790699999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5R,6R)-4-hydroxy-3,5,6-trimethyloxan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)

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PDB for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)
HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-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  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.667  -0.000   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  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+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    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    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 NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)
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SMILES for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)
C[C@H]1OC(=O)[C@H](C)[C@@H](O)[C@H]1C
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INCHI for NP0314202 ((3r,4s,5r,6r)-4-hydroxy-3,5,6-trimethyloxan-2-one)
InChI=1S/C8H14O3/c1-4-6(3)11-8(10)5(2)7(4)9/h4-7,9H,1-3H3/t4-,5+,6+,7-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H14O3
Average Mass158.1970 Da
Monoisotopic Mass158.09429 Da
IUPAC Name(3R,4S,5R,6R)-4-hydroxy-3,5,6-trimethyloxan-2-one
Traditional Name(3R,4S,5R,6R)-4-hydroxy-3,5,6-trimethyloxan-2-one
CAS Registry NumberNot Available
SMILES
C[C@H]1OC(=O)[C@H](C)[C@@H](O)[C@H]1C
InChI Identifier
InChI=1S/C8H14O3/c1-4-6(3)11-8(10)5(2)7(4)9/h4-7,9H,1-3H3/t4-,5+,6+,7-/m0/s1
InChI KeyWIPAYFJRYZXVMZ-WNJXEPBRSA-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
Streptomyces albidoflavusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassDelta valerolactones  
Direct ParentDelta valerolactones  
Alternative Parents
Substituents
  • Delta_valerolactone
    • 

  • Delta valerolactone
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP0.73ChemAxon
pKa (Strongest Acidic)14.37ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area46.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity39.79 m³·mol⁻¹ChemAxon
Polarizability16.61 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 ID8594868  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10419438  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]