NP-MRD: Showing NP-Card for (1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one (NP0163663)

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Record Information

Version

2.0

Created at

2022-09-02 22:22:35 UTC

Updated at

2022-09-02 22:22:35 UTC

NP-MRD ID

NP0163663

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one

Description

CHEMBL1912044 belongs to the class of organic compounds known as xanthanolides. These are sesquiterpenoids with a structure based on the xanthanolide skeleton consistsing of a cycloheptane ring usually attached to a four-carbon chain (at carbon 1 ) and a methyl group (at carbon 10), and fused to a five-member lactone ring (sharing carbons 7 and 8). The lactone ring can be conjugated with a methyl or methylene group at position 11. (1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one is found in Inula caspica. Based on a literature review very few articles have been published on CHEMBL1912044.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309032200222D          

 19 21  0  0  1  0            999 V2000
    0.9913   -2.4920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0898   -1.6729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4850   -1.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3245   -1.2713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8317   -0.3632    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6508   -0.4616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1842    0.1677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0088    0.1431    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3888    0.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5037   -0.5170    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1250    0.0259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9655    0.8353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5868    1.3781    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4273    2.1876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3675    1.1115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0915   -1.0959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2962   -1.3154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5426   -1.6511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8103   -1.2711    0.0000 C   0  0  2  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  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 10 16  1  0  0  0  0
 17 16  1  6  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19  2  1  6  0  0  0
  6 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0163663

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(O)CC[C@@]12O[C@@H]1C[C@H]1[C@@H](C[C@@H]2C)OC(=O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O4/c1-8-6-12-11(10(3)14(17)18-12)7-13-15(8,19-13)5-4-9(2)16/h8-9,11-13,16H,3-7H2,1-2H3/t8-,9?,11+,12+,13+,15-/m0/s1

> <INCHI_KEY>
GCZUNBFNRYZCOY-AREHDLCJSA-N

> <FORMULA>
C15H22O4

> <MOLECULAR_WEIGHT>
266.337

> <EXACT_MASS>
266.151809188

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
29.125728788849035

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,3R,5S,6S,8R)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0^{3,5}]undecan-10-one

> <ALOGPS_LOGP>
1.71

> <JCHEM_LOGP>
1.8562923626666663

> <ALOGPS_LOGS>
-2.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.659085251222354

> <JCHEM_PKA_STRONGEST_BASIC>
-2.510516111115342

> <JCHEM_POLAR_SURFACE_AREA>
59.06

> <JCHEM_REFRACTIVITY>
69.60340000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,3R,5S,6S,8R)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0^{3,5}]undecan-10-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       1.850  -4.652   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.034  -3.123   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.905  -2.075   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.606  -2.373   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.553  -0.678   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.082  -0.862   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.077   0.313   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.617   0.267   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.326   1.634   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.540  -0.965   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.700   0.048   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.402   1.559   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.562   2.573   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.264   4.083   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.019   2.075   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.637  -2.046   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.153  -2.456   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.746  -3.082   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.379  -2.373   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16   17                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   10   17                                                       
CONECT   17   16   10   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₂O₄

Average Mass

266.3370 Da

Monoisotopic Mass

266.15181 Da

IUPAC Name

(1R,3R,5S,6S,8R)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0^{3,5}]undecan-10-one

Traditional Name

(1R,3R,5S,6S,8R)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0^{3,5}]undecan-10-one

CAS Registry Number

Not Available

SMILES

CC(O)CC[C@@]12O[C@@H]1C[C@H]1[C@@H](C[C@@H]2C)OC(=O)C1=C

InChI Identifier

InChI=1S/C15H22O4/c1-8-6-12-11(10(3)14(17)18-12)7-13-15(8,19-13)5-4-9(2)16/h8-9,11-13,16H,3-7H2,1-2H3/t8-,9?,11+,12+,13+,15-/m0/s1

InChI Key

GCZUNBFNRYZCOY-AREHDLCJSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Inula caspica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthanolides. These are sesquiterpenoids with a structure based on the xanthanolide skeleton consistsing of a cycloheptane ring usually attached to a four-carbon chain (at carbon 1 ) and a methyl group (at carbon 10), and fused to a five-member lactone ring (sharing carbons 7 and 8). The lactone ring can be conjugated with a methyl or methylene group at position 11.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Xanthanolides

Alternative Parents

Substituents

Xanthanolide-skeleton
Sesquiterpenoid
Gamma butyrolactone
Oxolane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Oxirane
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Alcohol
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
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	1.71	ALOGPS
logP	1.86	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	15.66	ChemAxon
pKa (Strongest Basic)	-2.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	59.06 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.6 m³·mol⁻¹	ChemAxon
Polarizability	29.13 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

28483974

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56931704

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one (NP0163663)

MOL for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

3D MOL for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

3D SDF for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

3D-SDF for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

PDB for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

3D PDB for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

SMILES for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

INCHI for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

Structure for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)

3D Structure for NP0163663 ((1r,3r,5s,6s,8r)-5-(3-hydroxybutyl)-6-methyl-11-methylidene-4,9-dioxatricyclo[6.3.0.0³,⁵]undecan-10-one)