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Showing NP-Card for (1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one (NP0309827)

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Record Information
Version2.0
Created at2022-09-11 04:41:30 UTC
Updated at2022-09-11 04:41:30 UTC
NP-MRD IDNP0309827
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one
DescriptionQuinide 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. (1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one is found in Gardenia sootepensis. (1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one was first documented in 2015 (PMID: 25172718). Based on a literature review a small amount of articles have been published on Quinide (PMID: 35763924) (PMID: 35551255) (PMID: 31377616) (PMID: 27806409).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)


  Mrv1652309112206412D          

 12 13  0  0  1  0            999 V2000
   -0.5840    0.8521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1593    0.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1593   -0.3309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8044   -0.8453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0361    0.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8044    1.0085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6208    1.8128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087    0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9666    0.0816    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7916    0.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087   -0.6617    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1231   -1.3067    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  6  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
M  END
Download

3D MOL for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)

     RDKit          3D

 22 23  0  0  0  0  0  0  0  0999 V2000
   -2.3753   -0.6635   -1.9538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5714   -0.0554   -1.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136    0.9907   -1.5330 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0481    1.3890   -0.4059 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9315    1.0668    0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3530   -0.3237    0.2643 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4872   -0.6845    0.9246 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2457   -1.3092    0.4361 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0720   -0.8823   -0.0691 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0513   -1.3238    0.8546 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2813    0.5629   -0.2870 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0794    1.1271    0.7358 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3156    2.4475   -0.4192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4605    1.0661    1.7027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7887    1.7351    0.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9662   -1.4591    0.5819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2238   -1.5866    1.5315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673   -2.2582   -0.0728 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3171   -1.4523   -1.0131 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8816   -0.8336    0.7059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8777    0.7209   -1.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7600    1.7261    0.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  6  1  0
  6  7  1  1
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  4 11  1  0
 11 12  1  0
 11  9  1  0
  2  6  1  0
 10 20  1  0
  9 19  1  6
  8 17  1  0
  8 18  1  0
  7 16  1  0
  5 14  1  0
  5 15  1  0
  4 13  1  6
 11 21  1  6
 12 22  1  0
M  END
Download

3D SDF for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)


  Mrv1652309112206412D          

 12 13  0  0  1  0            999 V2000
   -0.5840    0.8521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1593    0.4941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1593   -0.3309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8044   -0.8453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0361    0.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8044    1.0085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6208    1.8128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087    0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9666    0.0816    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7916    0.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6087   -0.6617    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1231   -1.3067    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  6  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0309827

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1C[C@@]2(O)C[C@H](OC2=O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O5/c8-3-1-7(11)2-4(5(3)9)12-6(7)10/h3-5,8-9,11H,1-2H2/t3-,4-,5-,7+/m0/s1

> <INCHI_KEY>
QPJRIFFWEBJVFN-DRMQKGJZSA-N

> <FORMULA>
C7H10O5

> <MOLECULAR_WEIGHT>
174.152

> <EXACT_MASS>
174.052823422

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.456985142004607

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3S,4S,5S)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one

> <JCHEM_LOGP>
-2.030818708

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.201317838757337

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.139594415683735

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2318222033555264

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
36.212999999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3S,4S,5S)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)

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PDB for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-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  O   UNK     0      -1.090   1.591   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.297   0.922   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.297  -0.618   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.501  -1.578   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.934   0.152   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.501   1.883   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.159   3.384   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.003   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.671   0.152   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.211   0.152   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.003  -1.235   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.963  -2.439   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    2    7    8                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

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3D PDB for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)
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SMILES for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)
O[C@H]1C[C@@]2(O)C[C@H](OC2=O)[C@H]1O
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INCHI for NP0309827 ((1r,3s,4s,5s)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one)
InChI=1S/C7H10O5/c8-3-1-7(11)2-4(5(3)9)12-6(7)10/h3-5,8-9,11H,1-2H2/t3-,4-,5-,7+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H10O5
Average Mass174.1520 Da
Monoisotopic Mass174.05282 Da
IUPAC Name(1R,3S,4S,5S)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one
Traditional Name(1R,3S,4S,5S)-1,3,4-trihydroxy-6-oxabicyclo[3.2.1]octan-7-one
CAS Registry NumberNot Available
SMILES
O[C@H]1C[C@@]2(O)C[C@H](OC2=O)[C@H]1O
InChI Identifier
InChI=1S/C7H10O5/c8-3-1-7(11)2-4(5(3)9)12-6(7)10/h3-5,8-9,11H,1-2H2/t3-,4-,5-,7+/m0/s1
InChI KeyQPJRIFFWEBJVFN-DRMQKGJZSA-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
Gardenia sootepensisLOTUS 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
  • Oxepane
    • 

  • Gamma butyrolactone
    • 

  • Tetrahydrofuran
    • 

  • Tertiary alcohol
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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-2ChemAxon
pKa (Strongest Acidic)12.14ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.21 m³·mol⁻¹ChemAxon
Polarizability15.46 ųChemAxon
Number of Rings2ChemAxon
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 ID110594937  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkQuinic acid  
METLIN IDNot Available
PubChem Compound101711082  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Lin H, Tello E, Simons CT, Peterson DG: Identification of subthreshold chlorogenic acid lactones that contribute to flavor instability of ready-to-drink coffee. Food Chem. 2022 Nov 30;395:133555. doi: 10.1016/j.foodchem.2022.133555. Epub 2022  Jun 22. [PubMed:35763924  ] 
  2. Slimestad R, Rathe BA, Aesoy R, Diaz AEC, Herfindal L, Fossen T: A novel bicyclic lactone and other polyphenols from the commercially important vegetable Anthriscus cerefolium. Sci Rep. 2022 May 12;12(1):7805. doi: 10.1038/s41598-022-11923-0. [PubMed:35551255  ] 
  3. Sittipod S, Schwartz E, Paravisini L, Peterson DG: Identification of flavor modulating compounds that positively impact coffee quality. Food Chem. 2019 Dec 15;301:125250. doi: 10.1016/j.foodchem.2019.125250. Epub 2019  Jul 24. [PubMed:31377616  ] 
  4. Sinisi V, Stevaert A, Berti F, Forzato C, Benedetti F, Navarini L, Camps A, Persoons L, Vermeire K: Chlorogenic Compounds from Coffee Beans Exert Activity against Respiratory Viruses. Planta Med. 2017 May;83(7):615-623. doi: 10.1055/s-0042-119449. Epub 2016 Nov 2. [PubMed:27806409  ] 
  5. Sinisi V, Forzato C, Cefarin N, Navarini L, Berti F: Interaction of chlorogenic acids and quinides from coffee with human serum albumin. Food Chem. 2015 Feb 1;168:332-40. doi: 10.1016/j.foodchem.2014.07.080. Epub 2014  Jul 24. [PubMed:25172718  ] 
  6. LOTUS database [Link]