NP-MRD: Showing NP-Card for methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate (NP0226450)

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Record Information

Version

2.0

Created at

2022-09-06 05:29:41 UTC

Updated at

2022-09-06 05:29:41 UTC

NP-MRD ID

NP0226450

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate

Description

Alpha-Gardiol, also known as a-gardiol, belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate is found in Cordiera sessilis, Burchellia bubalina, Catunaregam nilotica, Rothmannia globosa and Tocoyena formosa. methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate was first documented in 2016 (PMID: 27431771). Based on a literature review very few articles have been published on alpha-Gardiol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062207292D          

 17 19  0  0  1  0            999 V2000
    4.5737    2.2383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9484    1.7002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017    0.8895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8804    0.6170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    0.3514    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6297   -0.4592    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4084   -0.7317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0044   -0.9973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2257   -0.7248    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0605   -0.7849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420   -0.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3673    0.5143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6623    0.9427    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5569    1.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3792    1.3849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977    0.6239    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0724    0.0858    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  5  3  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 16 15  1  6  0  0  0
  5 16  1  0  0  0  0
 17 16  1  6  0  0  0
  9 17  1  0  0  0  0
 12 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0226450

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@H]1[C@H]2C=C[C@]3(O)CO[C@H](O[C@@H]1O)[C@@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O6/c1-15-8(12)6-5-2-3-11(14)4-16-10(7(5)11)17-9(6)13/h2-3,5-7,9-10,13-14H,4H2,1H3/t5-,6-,7-,9+,10-,11+/m1/s1

> <INCHI_KEY>
QEGAWOPOQXLXMR-MCEKMFAVSA-N

> <FORMULA>
C11H14O6

> <MOLECULAR_WEIGHT>
242.227

> <EXACT_MASS>
242.079038171

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.452161156819304

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1R,4R,7S,8S,9S,11S)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0^{4,11}]undec-5-ene-8-carboxylate

> <JCHEM_LOGP>
-0.6467856339999993

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.251906961379152

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.83374965366003

> <JCHEM_PKA_STRONGEST_BASIC>
-3.571359831767161

> <JCHEM_POLAR_SURFACE_AREA>
85.22000000000001

> <JCHEM_REFRACTIVITY>
54.886599999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,4R,7S,8S,9S,11S)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0^{4,11}]undec-5-ene-8-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       8.538   4.178   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.370   3.174   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.657   1.660   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       9.110   1.152   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.489   0.656   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.776  -0.857   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.229  -1.366   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.608  -1.862   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.155  -1.353   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.980  -1.465   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.385  -0.045   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.552   0.960   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.236   1.760   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.906   2.459   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.441   2.585   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.036   1.165   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.868   0.160   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   16                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   17                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    5   17                                                  
CONECT   17   16    9   12                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Value	Source
a-Gardiol	Generator
Α-gardiol	Generator

Chemical Formula

C₁₁H₁₄O₆

Average Mass

242.2270 Da

Monoisotopic Mass

242.07904 Da

IUPAC Name

methyl (1R,4R,7S,8S,9S,11S)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0^{4,11}]undec-5-ene-8-carboxylate

Traditional Name

methyl (1R,4R,7S,8S,9S,11S)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0^{4,11}]undec-5-ene-8-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H]1[C@H]2C=C[C@]3(O)CO[C@H](O[C@@H]1O)[C@@H]23

InChI Identifier

InChI=1S/C11H14O6/c1-15-8(12)6-5-2-3-11(14)4-16-10(7(5)11)17-9(6)13/h2-3,5-7,9-10,13-14H,4H2,1H3/t5-,6-,7-,9+,10-,11+/m1/s1

InChI Key

QEGAWOPOQXLXMR-MCEKMFAVSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Alibertia sessilis	LOTUS Database	35616633
Burchellia bubalina	LOTUS Database	35616633
Catunaregam nilotica	LOTUS Database	35616633
Rothmannia globosa	LOTUS Database	35616633
Tocoyena formosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Iridoid-skeleton
Furopyran
Beta-hydroxy acid
Hydroxy acid
Pyran
Oxane
Furan
Methyl ester
Tertiary alcohol
Oxolane
Carboxylic acid ester
Hemiacetal
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	-0.65	ChemAxon
pKa (Strongest Acidic)	11.83	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	85.22 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	54.89 m³·mol⁻¹	ChemAxon
Polarizability	22.45 Å³	ChemAxon
Number of Rings	3	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

C00040869

Chemspider ID

28944853

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101936008

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chaipukdee N, Kanokmedhakul K, Kanokmedhakul S, Lekphrom R, Pyne SG: Two new bioactive iridoids from Rothmannia wittii. Fitoterapia. 2016 Sep;113:97-101. doi: 10.1016/j.fitote.2016.07.007. Epub 2016 Jul 16. [PubMed:27431771 ]
LOTUS database [Link]

Showing NP-Card for methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate (NP0226450)

MOL for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

3D MOL for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

3D SDF for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

3D-SDF for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

PDB for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

3D PDB for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

SMILES for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

INCHI for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

Structure for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)

3D Structure for NP0226450 (methyl (1r,4r,7s,8s,9s,11s)-4,9-dihydroxy-2,10-dioxatricyclo[5.3.1.0⁴,¹¹]undec-5-ene-8-carboxylate)