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Showing NP-Card for 4-hydroxy-5-(hydroxymethyl)oxolan-2-one (NP0256359)

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Record Information
Version2.0
Created at2022-09-07 21:09:33 UTC
Updated at2022-09-07 21:09:34 UTC
NP-MRD IDNP0256359
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-hydroxy-5-(hydroxymethyl)oxolan-2-one
Description2-Deoxy-L-ribono-1,4-lactone, also known as L-erythro-form, belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. 2-Deoxy-L-ribono-1,4-lactone is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 2-Deoxy-L-ribono-1,4-lactone has been detected, but not quantified in, herbs and spices. 4-hydroxy-5-(hydroxymethyl)oxolan-2-one is found in Clematis hexapetala, Clematis terniflora, Cnidium monnieri and Ophiocordyceps sinensis. This could make 2-deoxy-L-ribono-1,4-lactone a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)


  Mrv0541 05061307282D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
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3D MOL for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.8787   -1.6383    0.8888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8106   -1.0341    0.5822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8100    0.3012   -0.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3545    0.6622   -0.2045 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0796    1.3268   -1.3950 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3028   -0.7113   -0.1779 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7188   -0.5198    0.2982 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4002    0.1767   -0.6950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4951   -1.4132    0.7545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3045    0.9973    0.6515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3368    0.2532   -1.0420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0225    1.2341    0.6729 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1580    2.2772   -1.2673 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2891   -1.1342   -1.1848 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2612   -1.4787    0.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782    0.0338    1.2528 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1842    0.6670   -0.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  9  1  0
  9  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  8 17  1  0
  7 15  1  0
  7 16  1  0
  6 14  1  6
  3 10  1  0
  3 11  1  0
  4 12  1  1
  5 13  1  0
M  END
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3D SDF for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)


  Mrv0541 05061307282D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0256359

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(=O)CC1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O4/c6-2-4-3(7)1-5(8)9-4/h3-4,6-7H,1-2H2

> <INCHI_KEY>
YIXDEYPPAGPYDP-UHFFFAOYSA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.1146

> <EXACT_MASS>
132.042258744

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.983835311356083

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-5-(hydroxymethyl)oxolan-2-one

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-1.3997797833333334

> <ALOGPS_LOGS>
0.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.742787764595569

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.763343180584119

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9872108650610167

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
27.4781

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.72e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-5-(hydroxymethyl)oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)

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PDB for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    4    7                                                  
CONECT    4    2    3    9                                                  
CONECT    5    1    8    9                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)
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SMILES for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)
OCC1OC(=O)CC1O
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INCHI for NP0256359 (4-hydroxy-5-(hydroxymethyl)oxolan-2-one)
InChI=1S/C5H8O4/c6-2-4-3(7)1-5(8)9-4/h3-4,6-7H,1-2H2
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Synonyms
ValueSource
4,5-Dihydro-4-hydroxy-5-(hydroxymethyl)-2(3H)-furanoneHMDB
L-Erythro-formHMDB
Chemical FormulaC5H8O4
Average Mass132.1146 Da
Monoisotopic Mass132.04226 Da
IUPAC Name4-hydroxy-5-(hydroxymethyl)oxolan-2-one
Traditional Name4-hydroxy-5-(hydroxymethyl)oxolan-2-one
CAS Registry NumberNot Available
SMILES
OCC1OC(=O)CC1O
InChI Identifier
InChI=1S/C5H8O4/c6-2-4-3(7)1-5(8)9-4/h3-4,6-7H,1-2H2
InChI KeyYIXDEYPPAGPYDP-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
Clematis hexapetalaLOTUS Database
Clematis ternifloraLOTUS Database
Cnidium monnieriLOTUS Database
Ophiocordyceps sinensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassGamma butyrolactones  
Direct ParentGamma butyrolactones  
Alternative Parents
Substituents
  • Gamma butyrolactone
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-1.4ALOGPS
logP-1.4ChemAxon
logS0.87ALOGPS
pKa (Strongest Acidic)13.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity27.48 m³·mol⁻¹ChemAxon
Polarizability11.98 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033958  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012177  
KNApSAcK IDNot Available
Chemspider ID3826058  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4635870  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]