NP-MRD: Showing NP-Card for (4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one (NP0312872)

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Record Information

Version

2.0

Created at

2022-09-11 10:00:56 UTC

Updated at

2022-09-11 10:00:56 UTC

NP-MRD ID

NP0312872

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one

Description

9-Deoxygelsemide belongs to the class of organic compounds known as furopyrans. These are organic polycyclic compounds containing a furan ring fused to a pyran ring. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Pyran a six-membered heterocyclic, non-aromatic ring, made up of five carbon atoms and one oxygen atom and containing two double bonds. (4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one is found in Gelsemium elegans. (4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one was first documented in 2010 (PMID: 20038133). Based on a literature review very few articles have been published on 9-Deoxygelsemide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112212012D          

 14 16  0  0  1  0            999 V2000
    0.6213   -1.4832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0605   -0.7849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7420   -0.0239    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0609    0.1658    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3673    0.5143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5569    1.3172    0.0000 O   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
    2.8076    2.0900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6977    0.6239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4764    0.3514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6297   -0.4592    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0044   -0.9973    0.0000 C   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
    2.0724    0.0858    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  6  0  0  0
  2 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14  9  1  6  0  0  0
  5 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0312872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H](O)[C@@H]2OC(=O)C3=COC[C@H]1[C@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C10H12O4/c1-4-5-2-13-3-6-7(5)9(8(4)11)14-10(6)12/h3-5,7-9,11H,2H2,1H3/t4-,5-,7+,8+,9-/m1/s1

> <INCHI_KEY>
DHGUGNRVBRZGHD-JDAIJKHESA-N

> <FORMULA>
C10H12O4

> <MOLECULAR_WEIGHT>
196.202

> <EXACT_MASS>
196.073558866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.787158298161476

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R,5S,6R,7R,11S)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0^{4,11}]undec-1(10)-en-2-one

> <JCHEM_LOGP>
-0.06610795233333297

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.904622639361435

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2779180575433084

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
46.99920000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,6R,7R,11S)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0^{4,11}]undec-1(10)-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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  C   UNK     0       1.160  -2.769   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.980  -1.465   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.385  -0.045   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.114   0.309   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.552   0.960   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.906   2.459   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.441   2.585   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.241   3.901   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.036   1.165   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.489   0.656   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       6.776  -0.857   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.608  -1.862   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.155  -1.353   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.868   0.160   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    2   14                                                  
CONECT   14   13    9    5                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂O₄

Average Mass

196.2020 Da

Monoisotopic Mass

196.07356 Da

IUPAC Name

(4R,5S,6R,7R,11S)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0^{4,11}]undec-1(10)-en-2-one

Traditional Name

(4R,5S,6R,7R,11S)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0^{4,11}]undec-1(10)-en-2-one

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H](O)[C@@H]2OC(=O)C3=COC[C@H]1[C@H]23

InChI Identifier

InChI=1S/C10H12O4/c1-4-5-2-13-3-6-7(5)9(8(4)11)14-10(6)12/h3-5,7-9,11H,2H2,1H3/t4-,5-,7+,8+,9-/m1/s1

InChI Key

DHGUGNRVBRZGHD-JDAIJKHESA-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
Gelsemium elegans	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as furopyrans. These are organic polycyclic compounds containing a furan ring fused to a pyran ring. Furan is a five-membered aromatic ring with four carbon atoms and one oxygen atom. Pyran a six-membered heterocyclic, non-aromatic ring, made up of five carbon atoms and one oxygen atom and containing two double bonds.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Furopyrans

Sub Class

Not Available

Direct Parent

Furopyrans

Alternative Parents

Substituents

Furopyran
Pyran
Gamma butyrolactone
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Furan
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
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	-0.066	ChemAxon
pKa (Strongest Acidic)	13.9	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	47 m³·mol⁻¹	ChemAxon
Polarizability	18.79 Å³	ChemAxon
Number of Rings	3	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

61613055

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46176622

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

D'Alfonso A, Pasi M, Porta A, Zanoni G, Vidari G: Synthesis and assignment of absolute configuration of the iridoid 9-deoxygelsemide. Org Lett. 2010 Feb 5;12(3):596-9. doi: 10.1021/ol902809v. [PubMed:20038133 ]
LOTUS database [Link]

Showing NP-Card for (4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one (NP0312872)

MOL for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

3D MOL for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

3D SDF for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

3D-SDF for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

PDB for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

3D PDB for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

SMILES for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

INCHI for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

Structure for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)

3D Structure for NP0312872 ((4r,5s,6r,7r,11s)-5-hydroxy-6-methyl-3,9-dioxatricyclo[5.3.1.0⁴,¹¹]undec-1(10)-en-2-one)