NP-MRD: Showing NP-Card for (-)-Rabdoternin D (NP0075713)

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Record Information

Version

2.0

Created at

2022-04-28 20:57:33 UTC

Updated at

2022-04-28 20:57:33 UTC

NP-MRD ID

NP0075713

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Rabdoternin D

Description

(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1⁵,⁸.0¹,¹¹.0²,⁸]Octadecan-10-yl acetate belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D. (-)-Rabdoternin D is found in Isodon ternifolia, Isodon ternifolius and Isodon xerophilus. Based on a literature review very few articles have been published on (1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1⁵,⁸.0¹,¹¹.0²,⁸]Octadecan-10-yl acetate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282222572D          

 29 33  0  0  1  0            999 V2000
    7.3349   -0.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6004    0.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9763    0.5828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1341    0.4235    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8274   -0.4538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5193   -0.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9206   -0.6791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3622    0.1026    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7341    0.9050    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6118    1.1973    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8774    1.9784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3338    2.5990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5246    2.4385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5994    3.3801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1845    1.5203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4550    0.6284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1273   -0.0775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5366    0.3968    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8222   -0.0464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491    0.2416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0821   -0.8796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5820   -1.5689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4244   -1.3877    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8806   -2.0751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8131   -0.5412    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0842   -1.3204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4488    1.2171    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5371    1.1879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8120    1.3912    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
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  9 15  1  6  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
  8 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 21 19  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  1  0  0  0
 21 25  1  0  0  0  0
  8 25  1  0  0  0  0
 25 26  1  6  0  0  0
 18 27  1  1  0  0  0
  3 28  1  0  0  0  0
  3 29  1  0  0  0  0
M  END


  Mrv1652304282222572D          

 29 33  0  0  1  0            999 V2000
    7.3349   -0.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6004    0.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9763    0.5828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1341    0.4235    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8274   -0.4538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5193   -0.9618    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9206   -0.6791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3622    0.1026    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7341    0.9050    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6118    1.1973    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8774    1.9784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3338    2.5990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5246    2.4385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5994    3.3801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1845    1.5203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4550    0.6284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1273   -0.0775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5366    0.3968    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8222   -0.0464    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491    0.2416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0821   -0.8796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5820   -1.5689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4244   -1.3877    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8806   -2.0751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8131   -0.5412    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0842   -1.3204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4488    1.2171    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5371    1.1879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8120    1.3912    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
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  9 15  1  6  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
  8 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 21 19  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  1  0  0  0
 21 25  1  0  0  0  0
  8 25  1  0  0  0  0
 25 26  1  6  0  0  0
 18 27  1  1  0  0  0
  3 28  1  0  0  0  0
  3 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075713

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1[C@@H]2C(C)(C)CCC[C@@]22CO[C@@]1(O)[C@]13[C@H](O)[C@@H](C[C@H](O)[C@@H]21)C(=C)[C@H]3O

> <INCHI_IDENTIFIER>
InChI=1S/C22H32O7/c1-10-12-8-13(24)14-20-7-5-6-19(3,4)15(20)18(29-11(2)23)22(27,28-9-20)21(14,16(10)25)17(12)26/h12-18,24-27H,1,5-9H2,2-4H3/t12-,13-,14-,15+,16+,17+,18-,20-,21+,22+/m0/s1

> <INCHI_KEY>
SCQGHCFEGSHMDK-IHAUIWDBSA-N

> <FORMULA>
C22H32O7

> <MOLECULAR_WEIGHT>
408.491

> <EXACT_MASS>
408.21480337

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
39.18135854234115

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-10-yl acetate

> <ALOGPS_LOGP>
0.35

> <JCHEM_LOGP>
-0.01577473533333279

> <ALOGPS_LOGS>
-1.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.759756786957176

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.577542697626205

> <JCHEM_PKA_STRONGEST_BASIC>
-2.857025792165685

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
101.72230000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-10-yl acetate

> <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      13.692  -1.441   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.187   0.037   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.022   1.088   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.450   0.790   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.878  -0.847   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.169  -1.795   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.185  -1.268   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.143   0.192   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.837   1.689   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.475   2.235   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.971   3.693   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       9.956   4.851   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.446   4.552   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.452   6.309   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.811   2.838   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.183   1.173   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       9.571  -0.145   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.602   0.741   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.268  -0.087   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.825   0.451   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.753  -1.642   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.686  -2.929   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.259  -2.590   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.110  -3.874   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.118  -1.010   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       7.624  -2.465   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       6.438   2.272   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      14.069   2.217   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.716   2.597   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   28   29                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   17                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   23                                                  
CONECT    8    7    9   18   25                                             
CONECT    9    8   10   15   16                                             
CONECT   10    9    4   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    9                                                            
CONECT   16    9   17                                                       
CONECT   17   16    5                                                       
CONECT   18    8   19   27                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22    7   24                                                  
CONECT   24   23                                                            
CONECT   25   21    8   26                                                  
CONECT   26   25                                                            
CONECT   27   18                                                            
CONECT   28    3                                                            
CONECT   29    3                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   66    0
END

View in JSmol

Synonyms

Value	Source
(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-Tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1,.0,.0,]octadecan-10-yl acetic acid	Generator

Chemical Formula

C₂₂H₃₂O₇

Average Mass

408.4910 Da

Monoisotopic Mass

408.21480 Da

IUPAC Name

(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-10-yl acetate

Traditional Name

(1S,2S,3S,5S,7R,8S,9S,10S,11R,18R)-3,7,9,18-tetrahydroxy-12,12-dimethyl-6-methylidene-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-10-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1[C@@H]2C(C)(C)CCC[C@@]22CO[C@@]1(O)[C@]13[C@H](O)[C@@H](C[C@H](O)[C@@H]21)C(=C)[C@H]3O

InChI Identifier

InChI=1S/C22H32O7/c1-10-12-8-13(24)14-20-7-5-6-19(3,4)15(20)18(29-11(2)23)22(27,28-9-20)21(14,16(10)25)17(12)26/h12-18,24-27H,1,5-9H2,2-4H3/t12-,13-,14-,15+,16+,17+,18-,20-,21+,22+/m0/s1

InChI Key

SCQGHCFEGSHMDK-IHAUIWDBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Isodon ternifolia	Plant	KNApSAcK
Isodon ternifolius	LOTUS Database	35616633
Isodon xerophilus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Kaurane diterpenoids

Alternative Parents

Substituents

Kaurane diterpenoid
Oxane
Cyclic alcohol
Secondary alcohol
Hemiacetal
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
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	0.35	ALOGPS
logP	-0.016	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	10.58	ChemAxon
pKa (Strongest Basic)	-2.9	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	2	ChemAxon
Refractivity	101.72 m³·mol⁻¹	ChemAxon
Polarizability	39.18 Å³	ChemAxon
Number of Rings	5	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

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

162960911

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Rabdoternin D (NP0075713)

MOL for NP0075713 ((-)-Rabdoternin D)

3D MOL for NP0075713 ((-)-Rabdoternin D)

3D SDF for NP0075713 ((-)-Rabdoternin D)

3D-SDF for NP0075713 ((-)-Rabdoternin D)

PDB for NP0075713 ((-)-Rabdoternin D)

3D PDB for NP0075713 ((-)-Rabdoternin D)

SMILES for NP0075713 ((-)-Rabdoternin D)

INCHI for NP0075713 ((-)-Rabdoternin D)

Structure for NP0075713 ((-)-Rabdoternin D)

3D Structure for NP0075713 ((-)-Rabdoternin D)