NP-MRD: Showing NP-Card for (-)-Gardenate A (NP0072910)

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Record Information

Version

2.0

Created at

2022-04-28 18:11:22 UTC

Updated at

2022-04-28 18:11:22 UTC

NP-MRD ID

NP0072910

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Gardenate A

Description

Methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. (-)-Gardenate A is found in Gardenia jasminoides and Gardenia jasminoides ELLIS forma grandiflora (Loud.) MAKINO . Based on a literature review very few articles have been published on methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 36  0  0  0  0  0  0  0  0999 V2000
   -2.6579    1.6014    2.4188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7795    1.4622    1.3213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2626    1.0574    0.0888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5243    0.8241    0.0127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3764    0.9046   -1.0649 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3049    0.6675   -2.2786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0671   -0.4848   -2.0714 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3592   -0.1744   -0.9762 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0251   -1.5421   -0.7901 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0690   -2.3575   -0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9790   -1.5732    0.3223 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2211   -2.0982    0.9980 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3782   -1.6631    0.3917 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5883   -0.1490    0.1543 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7792    0.7149   -0.0909 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9682    1.3395   -1.1597 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7036    0.8199    0.9137 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8815    1.5891    0.8513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3285    2.4823    2.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2466    0.6478    2.5083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0303    1.6861    3.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8880    1.8930   -1.2983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9691    1.5631   -2.2985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6808    0.6094   -3.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3641   -0.8414   -2.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1986   -0.1708   -1.9603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2255   -1.9742   -1.8096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9202   -1.4899   -0.1748 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0894   -3.4811   -0.2194 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2454   -1.7417    2.0475 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1836   -3.1862    1.0288 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9982   -2.3919    0.1403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0668    0.2270    1.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0007    2.0797    1.8389 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7450    0.8687    0.7707 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9144    2.2820    0.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 14  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  5 22  1  6
  6 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  6
  9 27  1  0
  9 28  1  0
 10 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 14 33  1  1
 18 34  1  0
 18 35  1  0
 18 36  1  0
M  END


  Mrv1652304282220112D          

 18 18  0  0  1  0            999 V2000
   -0.9806    2.5546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5681    3.2691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2389    3.0975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3251    2.2771    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4286    1.9415    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6001    1.1345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0130    0.5825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3847    0.8796    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5563    0.0726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0396    1.8646    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0396    1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540    0.6271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540    2.2771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540    3.1021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4685    1.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1830    2.2771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8011    2.4684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1367    1.7147    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
  1  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4 10  1  1  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  1 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072910

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O6/c1-17-11(15)9(6-14)8-4-3-7(5-13)10(8)12(16)18-2/h3,8-10,13-14H,4-6H2,1-2H3/t8-,9+,10+/m0/s1

> <INCHI_KEY>
SDWHLKFQMBNHOO-IVZWLZJFSA-N

> <FORMULA>
C12H18O6

> <MOLECULAR_WEIGHT>
258.27

> <EXACT_MASS>
258.1103383

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.063601394619532

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate

> <ALOGPS_LOGP>
-0.02

> <JCHEM_LOGP>
-0.988394473333333

> <ALOGPS_LOGS>
-1.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.481632459329127

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.875253357444986

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7017962599466276

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
63.12060000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.58e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate

> <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      -1.830   4.769   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.060   6.102   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.446   5.782   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.607   4.251   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.800   3.624   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.120   2.118   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.024   1.087   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.585   1.642   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.905   0.136   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.941   3.481   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.941   1.941   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.274   1.171   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.274   4.251   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.274   5.791   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.608   3.481   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       5.942   4.251   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.362   4.608   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -3.988   3.201   0.000  0.00  0.00           O+0
CONECT    1    2    5   17                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    4   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
CONECT   17    1   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
Methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylic acid	Generator

Chemical Formula

C₁₂H₁₈O₆

Average Mass

258.2700 Da

Monoisotopic Mass

258.11034 Da

IUPAC Name

methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate

Traditional Name

methyl (1S,5R)-5-[(2S)-3-hydroxy-1-methoxy-1-oxopropan-2-yl]-2-(hydroxymethyl)cyclopent-2-ene-1-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H](CO)[C@@H]1CC=C(CO)[C@H]1C(=O)OC

InChI Identifier

InChI=1S/C12H18O6/c1-17-11(15)9(6-14)8-4-3-7(5-13)10(8)12(16)18-2/h3,8-10,13-14H,4-6H2,1-2H3/t8-,9+,10+/m0/s1

InChI Key

SDWHLKFQMBNHOO-IVZWLZJFSA-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
Gardenia jasminoides	LOTUS Database	35616633
Gardenia jasminoides ELLIS forma grandiflora (Loud.) MAKINO	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Dicarboxylic acid or derivatives
Methyl ester
Carboxylic acid ester
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	-0.02	ALOGPS
logP	-0.99	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	14.88	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	63.12 m³·mol⁻¹	ChemAxon
Polarizability	26.06 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

154496615

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Gardenate A (NP0072910)

MOL for NP0072910 ((-)-Gardenate A)

3D MOL for NP0072910 ((-)-Gardenate A)

3D SDF for NP0072910 ((-)-Gardenate A)

3D-SDF for NP0072910 ((-)-Gardenate A)

PDB for NP0072910 ((-)-Gardenate A)

3D PDB for NP0072910 ((-)-Gardenate A)

SMILES for NP0072910 ((-)-Gardenate A)

INCHI for NP0072910 ((-)-Gardenate A)

Structure for NP0072910 ((-)-Gardenate A)

3D Structure for NP0072910 ((-)-Gardenate A)