NP-MRD: Showing NP-Card for (+)-Goniodiol (NP0075379)

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Record Information

Version

1.0

Created at

2022-04-28 20:39:37 UTC

Updated at

2022-04-28 20:39:37 UTC

NP-MRD ID

NP0075379

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Goniodiol

Description

7-Epi-Goniodiol belongs to the class of organic compounds known as dihydropyranones. Dihydropyranones are compounds containing a hydrogenated pyran ring which bears a ketone, and contains one double bond. (+)-Goniodiol is found in Goniothalamus cardiopetalus. It was first documented in 2008 (PMID: 18776681). Based on a literature review very few articles have been published on 7-epi-Goniodiol (PMID: 34878452).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
   -2.6858    2.8464    0.4882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8001    1.6050    0.2740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5611    0.7315    1.1438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6510   -0.5456    0.8817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9936   -1.1448   -0.2909 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8632   -0.3099   -0.8357 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5817   -0.4809   -0.0463 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2203   -1.8369   -0.0188 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4876    0.2726   -0.7868 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5558   -0.2598   -2.0864 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7991    0.2363   -0.1389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0299   -0.1788    1.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138   -0.1676    1.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3999    0.2490    0.9008 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1686    0.6634   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8948    0.6505   -0.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1761    1.0645   -0.8296 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0474    1.1851    2.0141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2312   -1.1924    1.5517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7746   -1.1680   -1.1079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7107   -2.1959   -0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6329   -0.5770   -1.8874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7189   -0.1567    0.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6895   -2.3372   -0.7401 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1839    1.3341   -0.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6751    0.4711   -2.7560 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1694   -0.4975    1.7206 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4943   -0.4969    2.6809 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4046    0.2607    1.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0108    0.9899   -0.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7506    0.9860   -1.9114 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 17  1  0
 16 11  1  0
 17  6  1  0
  8 24  1  0
  7 23  1  1
  9 25  1  6
 10 26  1  0
 12 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  0
 16 31  1  0
  6 22  1  6
  5 20  1  0
  5 21  1  0
  4 19  1  0
  3 18  1  0
M  END


  Mrv1652304282222392D          

 17 18  0  0  1  0            999 V2000
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    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  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  4  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
  9 16  1  6  0  0  0
  8 17  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0075379

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]([C@H](O)C1=CC=CC=C1)[C@H]1CC=CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C13H14O4/c14-11-8-4-7-10(17-11)13(16)12(15)9-5-2-1-3-6-9/h1-6,8,10,12-13,15-16H,7H2/t10-,12-,13-/m1/s1

> <INCHI_KEY>
RTNQVKQMVIXUPZ-RAIGVLPGSA-N

> <FORMULA>
C13H14O4

> <MOLECULAR_WEIGHT>
234.251

> <EXACT_MASS>
234.089208931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.33394335591561

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R)-6-[(1S,2R)-1,2-dihydroxy-2-phenylethyl]-5,6-dihydro-2H-pyran-2-one

> <ALOGPS_LOGP>
0.81

> <JCHEM_LOGP>
1.3488470969999997

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.388286152787586

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.913864910701086

> <JCHEM_PKA_STRONGEST_BASIC>
-3.495487692151962

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
62.210200000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6R)-6-[(1S,2R)-1,2-dihydroxy-2-phenylethyl]-5,6-dihydropyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    4    9   17                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16    9                                                            
CONECT   17    8                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₄O₄

Average Mass

234.2510 Da

Monoisotopic Mass

234.08921 Da

IUPAC Name

(6R)-6-[(1S,2R)-1,2-dihydroxy-2-phenylethyl]-5,6-dihydro-2H-pyran-2-one

Traditional Name

(6R)-6-[(1S,2R)-1,2-dihydroxy-2-phenylethyl]-5,6-dihydropyran-2-one

CAS Registry Number

Not Available

SMILES

O[C@@H]([C@H](O)C1=CC=CC=C1)[C@H]1CC=CC(=O)O1

InChI Identifier

InChI=1S/C13H14O4/c14-11-8-4-7-10(17-11)13(16)12(15)9-5-2-1-3-6-9/h1-6,8,10,12-13,15-16H,7H2/t10-,12-,13-/m1/s1

InChI Key

RTNQVKQMVIXUPZ-RAIGVLPGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Goniothalamus cardiopetalus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dihydropyranones. Dihydropyranones are compounds containing a hydrogenated pyran ring which bears a ketone, and contains one double bond.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrans

Sub Class

Pyranones and derivatives

Direct Parent

Dihydropyranones

Alternative Parents

Substituents

Dihydropyranone
Monocyclic benzene moiety
Benzenoid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
1,2-diol
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Aromatic alcohol
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.81	ALOGPS
logP	1.35	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.91	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	62.21 m³·mol⁻¹	ChemAxon
Polarizability	23.33 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

9531671

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11356744

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Xu Q, Li J, Li X, Hu L: Annulation-retro-Claisen cascade of bifunctional peroxides for the synthesis of lactone natural products. Chem Commun (Camb). 2021 Dec 23;58(2):274-277. doi: 10.1039/d1cc06207g. [PubMed:34878452 ]
Yoshida T, Yamauchi S, Tago R, Maruyama M, Akiyama K, Sugahara T, Kishida T, Koba Y: Syntheses of all stereoisomers of goniodiol from yeast-reduction products and their antimicrobiological activity. Biosci Biotechnol Biochem. 2008 Sep;72(9):2342-52. doi: 10.1271/bbb.80262. Epub 2008 Sep 7. [PubMed:18776681 ]

Showing NP-Card for (+)-Goniodiol (NP0075379)

MOL for NP0075379 ((+)-Goniodiol)

3D MOL for NP0075379 ((+)-Goniodiol)

3D SDF for NP0075379 ((+)-Goniodiol)

3D-SDF for NP0075379 ((+)-Goniodiol)

PDB for NP0075379 ((+)-Goniodiol)

3D PDB for NP0075379 ((+)-Goniodiol)

SMILES for NP0075379 ((+)-Goniodiol)

INCHI for NP0075379 ((+)-Goniodiol)

Structure for NP0075379 ((+)-Goniodiol)

3D Structure for NP0075379 ((+)-Goniodiol)