NP-MRD: Showing NP-Card for Cedronolactone A (NP0083038)

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Record Information

Version

2.0

Created at

2022-04-29 04:05:18 UTC

Updated at

2022-04-29 04:05:18 UTC

NP-MRD ID

NP0083038

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cedronolactone A

Description

(1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0¹,⁵.0⁴,⁸.0¹¹,¹⁶]Octadecan-6-one belongs to the class of organic compounds known as quassinoids. These are a group of compounds chemically degraded from triterpenes. According to their basic skeleton, quassinoids are categorized into five distinct groups, C-18, C-19, C-20, C-22 and C-25 types. The C-20 quassinoids can be further classified into two types, tetracyclic and the pentacyclic. The tetracyclic variety does not have oxygenation at C-20, while the pentacyclic quassinoids possess additional oxygenation at C-20 that allows for the formation of an additional ring. Cedronolactone A is found in Simba cedron. Based on a literature review very few articles have been published on (1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0¹,⁵.0⁴,⁸.0¹¹,¹⁶]Octadecan-6-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292206052D          

 26 30  0  0  1  0            999 V2000
   -0.4619   -0.9332    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1724   -0.2050    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5706    0.2335    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8884    0.9888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7024    1.1173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2490    0.4862    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0540    0.6666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6128    0.0596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3665   -0.7278    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5614   -0.9082    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0027   -0.3012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1980   -0.4444    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0376   -1.3194    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1854   -1.5075    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4736   -0.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4681   -0.4337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2930   -0.4265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6313   -1.8922    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7390   -1.0829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3151   -1.6956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9252   -1.3348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3004    1.4539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3797    1.6382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3527    0.4784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628   -0.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0847   -1.4743    0.0000 C   0  0  0  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  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12  3  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  1 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
  2 16  1  6  0  0  0
 16 17  2  0  0  0  0
 13 18  1  6  0  0  0
 11 19  1  1  0  0  0
 10 20  1  6  0  0  0
  9 21  1  6  0  0  0
  7 22  1  1  0  0  0
  4 23  1  6  0  0  0
  3 24  1  6  0  0  0
 24 25  1  0  0  0  0
  1 25  1  0  0  0  0
  1 26  1  6  0  0  0
M  END


  Mrv1652304292206052D          

 26 30  0  0  1  0            999 V2000
   -0.4619   -0.9332    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1724   -0.2050    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5706    0.2335    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8884    0.9888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7024    1.1173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2490    0.4862    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0540    0.6666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6128    0.0596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3665   -0.7278    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5614   -0.9082    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0027   -0.3012    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1980   -0.4444    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0376   -1.3194    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1854   -1.5075    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4736   -0.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4681   -0.4337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2930   -0.4265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6313   -1.8922    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7390   -1.0829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3151   -1.6956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9252   -1.3348    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3004    1.4539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3797    1.6382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3527    0.4784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628   -0.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0847   -1.4743    0.0000 C   0  0  0  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  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12  3  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  1 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
  2 16  1  6  0  0  0
 16 17  2  0  0  0  0
 13 18  1  6  0  0  0
 11 19  1  1  0  0  0
 10 20  1  6  0  0  0
  9 21  1  6  0  0  0
  7 22  1  1  0  0  0
  4 23  1  6  0  0  0
  3 24  1  6  0  0  0
 24 25  1  0  0  0  0
  1 25  1  0  0  0  0
  1 26  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0083038

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@H](O)[C@H](O)[C@@]2(C)[C@H]1C[C@@H](O)[C@]13CO[C@]4(C)[C@@H](OC(=O)[C@H]14)[C@@H](O)[C@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C19H28O7/c1-7-4-9(20)14(23)17(2)8(7)5-10(21)19-6-25-18(3)13(19)16(24)26-15(18)11(22)12(17)19/h7-15,20-23H,4-6H2,1-3H3/t7-,8-,9-,10+,11-,12+,13-,14-,15-,17-,18-,19-/m0/s1

> <INCHI_KEY>
QVRFHIZYHPQMDT-WREABGOASA-N

> <FORMULA>
C19H28O7

> <MOLECULAR_WEIGHT>
368.426

> <EXACT_MASS>
368.183503242

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
37.916921772180615

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0^{1,5}.0^{4,8}.0^{11,16}]octadecan-6-one

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-1.237041003666667

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.922930698984988

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.363637045204406

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9850211985343638

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
88.30330000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.88e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0^{1,5}.0^{4,8}.0^{11,16}]octadecan-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      -0.862  -1.742   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.322  -0.383   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.065   0.436   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.658   1.846   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.178   2.086   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.198   0.908   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.701   1.244   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.744   0.111   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.284  -1.359   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.781  -1.695   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.738  -0.562   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.236  -0.830   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.937  -2.463   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.346  -2.814   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.884  -1.472   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.874  -0.810   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.414  -0.796   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.045  -3.532   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.246  -2.021   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.322  -3.165   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.327  -2.492   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.161   2.714   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.709   3.058   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.658   0.893   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.797  -0.332   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -2.025  -2.752   0.000  0.00  0.00           C+0
CONECT    1    2   14   25   26                                             
CONECT    2    1    3   16                                                  
CONECT    3    2    4   12   24                                             
CONECT    4    3    5   23                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8   22                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   21                                                  
CONECT   10    9   11   20                                                  
CONECT   11   10    6   12   19                                             
CONECT   12   11    3   13                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13    1   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15    2   17                                                  
CONECT   17   16                                                            
CONECT   18   13                                                            
CONECT   19   11                                                            
CONECT   20   10                                                            
CONECT   21    9                                                            
CONECT   22    7                                                            
CONECT   23    4                                                            
CONECT   24    3   25                                                       
CONECT   25   24    1                                                       
CONECT   26    1                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₈O₇

Average Mass

368.4260 Da

Monoisotopic Mass

368.18350 Da

IUPAC Name

(1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0^{1,5}.0^{4,8}.0^{11,16}]octadecan-6-one

Traditional Name

(1S,4S,5R,8S,9S,10R,11S,12R,13S,15S,16S,18R)-9,12,13,18-tetrahydroxy-4,11,15-trimethyl-3,7-dioxapentacyclo[8.8.0.0^{1,5}.0^{4,8}.0^{11,16}]octadecan-6-one

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@H](O)[C@H](O)[C@@]2(C)[C@H]1C[C@@H](O)[C@]13CO[C@]4(C)[C@@H](OC(=O)[C@H]14)[C@@H](O)[C@H]23

InChI Identifier

InChI=1S/C19H28O7/c1-7-4-9(20)14(23)17(2)8(7)5-10(21)19-6-25-18(3)13(19)16(24)26-15(18)11(22)12(17)19/h7-15,20-23H,4-6H2,1-3H3/t7-,8-,9-,10+,11-,12+,13-,14-,15-,17-,18-,19-/m0/s1

InChI Key

QVRFHIZYHPQMDT-WREABGOASA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Simba cedron	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quassinoids. These are a group of compounds chemically degraded from triterpenes. According to their basic skeleton, quassinoids are categorized into five distinct groups, C-18, C-19, C-20, C-22 and C-25 types. The C-20 quassinoids can be further classified into two types, tetracyclic and the pentacyclic. The tetracyclic variety does not have oxygenation at C-20, while the pentacyclic quassinoids possess additional oxygenation at C-20 that allows for the formation of an additional ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Quassinoids

Alternative Parents

Substituents

C-19 quassinoid skeleton
Furofuran
Caprolactone
Oxepane
Gamma butyrolactone
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
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	-0.2	ALOGPS
logP	-1.2	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	13.36	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	88.3 m³·mol⁻¹	ChemAxon
Polarizability	37.92 Å³	ChemAxon
Number of Rings	5	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

163105749

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cedronolactone A (NP0083038)

MOL for NP0083038 (Cedronolactone A)

3D MOL for NP0083038 (Cedronolactone A)

3D SDF for NP0083038 (Cedronolactone A)

3D-SDF for NP0083038 (Cedronolactone A)

PDB for NP0083038 (Cedronolactone A)

3D PDB for NP0083038 (Cedronolactone A)

SMILES for NP0083038 (Cedronolactone A)

INCHI for NP0083038 (Cedronolactone A)

Structure for NP0083038 (Cedronolactone A)

3D Structure for NP0083038 (Cedronolactone A)