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Showing NP-Card for (2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one (NP0246675)

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Record Information
Version2.0
Created at2022-09-07 08:13:30 UTC
Updated at2022-09-07 08:13:30 UTC
NP-MRD IDNP0246675
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one
DescriptionHaliclonol belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms. (2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one is found in Haliclona tubifera. (2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one was first documented in 2010 (PMID: 20645241). Based on a literature review very few articles have been published on Haliclonol.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)


  Mrv1652309072210132D          

 10 10  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    0.7145   -0.4125    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
    0.0000    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
Download

3D MOL for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    1.5567   -0.7513    2.1849 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1849   -0.5176    1.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0968   -1.2643    0.4106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7330   -0.4763   -0.5367 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0923   -0.1373    0.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8864    0.3633   -0.9376 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1889    0.6348   -1.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6450    1.3813   -0.3042 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8261    0.5651    0.2297 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4628    0.0210   -0.8884 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5641   -1.7161    1.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5683   -2.1529   -0.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9979   -1.1674   -1.3929 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9934    0.5648    0.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -1.0841    0.4479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8566    1.3653   -0.9645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1765    1.9273    0.5358 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1088    2.1653   -0.9524 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5053    1.1868    0.8110 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7353   -0.9077   -0.7377 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2  9  1  0
  9 10  1  0
  9  8  1  0
  8  7  1  0
  7  4  1  0
  6 16  1  0
  5 14  1  0
  5 15  1  0
  4 13  1  6
  3 11  1  0
  3 12  1  0
  9 19  1  1
 10 20  1  0
  8 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)


  Mrv1652309072210132D          

 10 10  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    0.7145   -0.4125    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
    0.0000    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
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0246675

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1CC(=O)[C@@H](O)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O4/c7-2-4-1-5(8)6(9)3-10-4/h4,6-7,9H,1-3H2/t4-,6-/m0/s1

> <INCHI_KEY>
PBWGPVKLJDUIJH-NJGYIYPDSA-N

> <FORMULA>
C6H10O4

> <MOLECULAR_WEIGHT>
146.142

> <EXACT_MASS>
146.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.657145707652449

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5S)-5-hydroxy-2-(hydroxymethyl)oxan-4-one

> <JCHEM_LOGP>
-1.2379806413333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.188803466074948

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.58935940937237

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9473123486477295

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
32.788599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,5S)-5-hydroxy-2-(hydroxymethyl)oxan-4-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)

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PDB for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         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       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.334  -0.770   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  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    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    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 NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)
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SMILES for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)
OC[C@@H]1CC(=O)[C@@H](O)CO1
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INCHI for NP0246675 ((2s,5s)-5-hydroxy-2-(hydroxymethyl)oxan-4-one)
InChI=1S/C6H10O4/c7-2-4-1-5(8)6(9)3-10-4/h4,6-7,9H,1-3H2/t4-,6-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H10O4
Average Mass146.1420 Da
Monoisotopic Mass146.05791 Da
IUPAC Name(2S,5S)-5-hydroxy-2-(hydroxymethyl)oxan-4-one
Traditional Name(2S,5S)-5-hydroxy-2-(hydroxymethyl)oxan-4-one
CAS Registry NumberNot Available
SMILES
OC[C@@H]1CC(=O)[C@@H](O)CO1
InChI Identifier
InChI=1S/C6H10O4/c7-2-4-1-5(8)6(9)3-10-4/h4,6-7,9H,1-3H2/t4-,6-/m0/s1
InChI KeyPBWGPVKLJDUIJH-NJGYIYPDSA-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
Haliclona tubiferaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxanes. Oxanes are compounds containing an oxane (tetrahydropyran) ring, which is a six-member saturated aliphatic heterocycle with one oxygen atom and five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassOxanes  
Sub ClassNot Available
Direct ParentOxanes  
Alternative Parents
Substituents
  • Oxane
    • 

  • Cyclic ketone
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Dialkyl ether
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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
logP-1.2ChemAxon
pKa (Strongest Acidic)12.59ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.79 m³·mol⁻¹ChemAxon
Polarizability13.66 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 ID155509  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound178653  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Fiskesund R, Abeyama K, Yoshinaga K, Abe J, Yuan Y, Yu S: 1,5-anhydro-D-fructose and its derivatives: biosynthesis, preparation and potential medical applications. Planta Med. 2010 Oct;76(15):1635-41. doi: 10.1055/s-0030-1250120. Epub 2010 Jul 19. [PubMed:20645241  ] 
  2. LOTUS database [Link]