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Showing NP-Card for Gardendiol (NP0071265)

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Record Information
Version2.0
Created at2022-04-28 16:39:23 UTC
Updated at2022-04-28 16:39:23 UTC
NP-MRD IDNP0071265
Secondary Accession NumbersNone
Natural Product Identification
Common NameGardendiol
Description(4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. Gardendiol is found in Cymbaria mongolica, Gardenia jasminoides and Genipa americana . Based on a literature review very few articles have been published on (4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0071265 (Gardendiol)


  Mrv1652304282218392D          

 14 15  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    3.5854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  6 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  5 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for NP0071265 (Gardendiol)

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.7674   -1.5550    1.3807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6979   -0.8966    1.4390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5559   -1.3307    2.1004 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7165   -1.1394    1.5037 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4563   -0.7259    0.0934 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6275   -0.2964   -0.6724 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0072   -0.8372   -0.5210 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5217   -0.6408    0.7515 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2206    0.6378   -1.5190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2668    0.8843   -1.3306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3170    0.5764    0.1420 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6219    0.4319    0.7678 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8170    0.6948   -0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8706    1.9562   -0.6205 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2720   -0.3142    2.0019 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3363   -2.0602    1.5342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1884   -1.4437   -0.4559 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9552   -1.9422   -0.6744 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7104   -0.4474   -1.2734 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9284    0.2399    0.8602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8744    1.1333   -2.2276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7958    0.1801   -1.9666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4067    1.9505   -1.5709 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3463    1.3383    0.6413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6891    1.1733    1.6221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7930   -0.0739   -0.9243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7648    0.4980    0.4426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4205    2.0087   -1.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  6  2  0
  6  7  1  0
  7  8  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 12  1  0
  5 11  1  0
 14 28  1  0
 13 26  1  0
 13 27  1  0
 12 25  1  1
 11 24  1  1
 10 22  1  0
 10 23  1  0
  9 21  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  5 17  1  6
  4 15  1  0
  4 16  1  0
M  END
Download

3D SDF for NP0071265 (Gardendiol)


  Mrv1652304282218392D          

 14 15  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    3.5854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  6 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  5 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0071265

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1[C@@H]2CC=C(CO)[C@H]2COC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14O4/c11-3-6-1-2-7-8(4-12)10(13)14-5-9(6)7/h1,7-9,11-12H,2-5H2/t7-,8+,9+/m0/s1

> <INCHI_KEY>
RQRMWYOWQUEKAS-DJLDLDEBSA-N

> <FORMULA>
C10H14O4

> <MOLECULAR_WEIGHT>
198.218

> <EXACT_MASS>
198.089208931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.20962754542819

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-0.910161764333333

> <ALOGPS_LOGS>
-1.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.488527844311012

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.883394424776878

> <JCHEM_PKA_STRONGEST_BASIC>
-2.701478857886163

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
50.250600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0071265 (Gardendiol)

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PDB for NP0071265 (Gardendiol)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       6.258   2.073   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   5.923   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.258   6.693   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.680  -1.012   0.000  0.00  0.00           O+0
CONECT    1    2    3    7                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    5   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for NP0071265 (Gardendiol)
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SMILES for NP0071265 (Gardendiol)
OC[C@@H]1[C@@H]2CC=C(CO)[C@H]2COC1=O
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INCHI for NP0071265 (Gardendiol)
InChI=1S/C10H14O4/c11-3-6-1-2-7-8(4-12)10(13)14-5-9(6)7/h1,7-9,11-12H,2-5H2/t7-,8+,9+/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC10H14O4
Average Mass198.2180 Da
Monoisotopic Mass198.08921 Da
IUPAC Name(4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one
Traditional Name(4S,4aR,7aS)-4,7-bis(hydroxymethyl)-1H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one
CAS Registry NumberNot Available
SMILES
OC[C@@H]1[C@@H]2CC=C(CO)[C@H]2COC1=O
InChI Identifier
InChI=1S/C10H14O4/c11-3-6-1-2-7-8(4-12)10(13)14-5-9(6)7/h1,7-9,11-12H,2-5H2/t7-,8+,9+/m0/s1
InChI KeyRQRMWYOWQUEKAS-DJLDLDEBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cymbaria mongolicaPlant
Gardenia jasminoidesPlant
Genipa americanaPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassTerpene lactones  
Direct ParentTerpene lactones  
Alternative Parents
Substituents
  • Terpene lactone
    • 

  • Iridoid-skeleton
    • 

  • Monoterpenoid
    • 

  • Bicyclic monoterpenoid
    • 

  • Delta_valerolactone
    • 

  • Delta valerolactone
    • 

  • Oxane
    • 

  • Lactone
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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-0.2ALOGPS
logP-0.91ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)14.88ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity50.25 m³·mol⁻¹ChemAxon
Polarizability20.21 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound160701616  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References