NP-MRD: Showing NP-Card for methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate (NP0170050)

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Record Information

Version

2.0

Created at

2022-09-03 06:07:04 UTC

Updated at

2022-09-03 06:07:04 UTC

NP-MRD ID

NP0170050

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate

Description

CHEMBL2113369 belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations. methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate is found in Salvia divinorum. Based on a literature review very few articles have been published on CHEMBL2113369.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032208072D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309032208072D          

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    1.5395   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.7770    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -3.4914    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  2  0  0  0  0
  5  3  1  6  0  0  0
  5  6  1  0  0  0  0
  6  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
  9 11  2  0  0  0  0
  7 12  1  0  0  0  0
 12 13  2  0  0  0  0
 14 12  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 19 20  1  1  0  0  0
 19 21  1  1  0  0  0
 21 22  1  1  0  0  0
 22 23  1  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 26 27  1  0  0  0  0
 25 28  1  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  1  0  0  0
 18 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 33 31  1  6  0  0  0
 15 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
  5 36  1  0  0  0  0
 14 36  1  0  0  0  0
 36 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0170050

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1O[C@H](OC)[C@](O)([C@@H]1O)[C@H]1CC(=O)[C@@H]2CC[C@@]3(C)[C@@H](C[C@H](OC(C)=O)C(=O)[C@@H]3[C@@]2(C)C1)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C26H38O11/c1-12(27)36-17-10-15(21(31)33-4)24(2)8-7-14-16(28)9-13(11-25(14,3)19(24)18(17)29)26(32)20(30)22(34-5)37-23(26)35-6/h13-15,17,19-20,22-23,30,32H,7-11H2,1-6H3/t13-,14-,15-,17-,19-,20+,22+,23-,24-,25-,26+/m0/s1

> <INCHI_KEY>
ODBHOLKTMJCQDG-RRQPKOPKSA-N

> <FORMULA>
C26H38O11

> <MOLECULAR_WEIGHT>
526.579

> <EXACT_MASS>
526.241412044

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.91579004800958

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1R,3S,4aR,4bS,6R,8aR,10aR)-3-(acetyloxy)-6-[(2S,3R,4S,5R)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-tetradecahydrophenanthrene-1-carboxylate

> <ALOGPS_LOGP>
0.90

> <JCHEM_LOGP>
0.9794021659999995

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.08444947117399

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.656415479486963

> <JCHEM_PKA_STRONGEST_BASIC>
-3.903573244353812

> <JCHEM_POLAR_SURFACE_AREA>
154.89000000000001

> <JCHEM_REFRACTIVITY>
125.09679999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,3S,4aR,4bS,6R,8aR,10aR)-3-(acetyloxy)-6-[(2S,3R,4S,5R)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate

> <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      -2.516  -7.851   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.746  -6.517   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.206  -6.517   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.564  -7.851   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.564  -5.184   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.206  -3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.564  -2.516   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.206  -1.183   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.746  -1.183   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.516  -2.516   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.516   0.151   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.104  -2.516   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.874  -1.183   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.874  -3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.414  -3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.644  -2.516   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.184  -2.516   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.724  -2.516   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.494  -1.183   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.740  -2.088   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.087  -0.556   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.753  -1.326   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.419  -0.556   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.248   0.975   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.754   1.295   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.381   2.702   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.912   2.863   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.524  -0.038   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.056  -0.199   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       7.494  -3.850   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.724  -5.184   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       7.494  -6.517   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.184  -5.184   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.414  -6.517   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.874  -6.517   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.104  -5.184   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.334  -6.517   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   36                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   36                                                  
CONECT   15   14   16   17   33                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   30                                                  
CONECT   19   18   20   21   28                                             
CONECT   20   19                                                            
CONECT   21   19   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   19   29                                                  
CONECT   29   28                                                            
CONECT   30   18   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   15   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35    5   14   37                                             
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₈O₁₁

Average Mass

526.5790 Da

Monoisotopic Mass

526.24141 Da

IUPAC Name

methyl (1R,3S,4aR,4bS,6R,8aR,10aR)-3-(acetyloxy)-6-[(2S,3R,4S,5R)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-tetradecahydrophenanthrene-1-carboxylate

Traditional Name

methyl (1R,3S,4aR,4bS,6R,8aR,10aR)-3-(acetyloxy)-6-[(2S,3R,4S,5R)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate

CAS Registry Number

Not Available

SMILES

CO[C@@H]1O[C@H](OC)[C@](O)([C@@H]1O)[C@H]1CC(=O)[C@@H]2CC[C@@]3(C)[C@@H](C[C@H](OC(C)=O)C(=O)[C@@H]3[C@@]2(C)C1)C(=O)OC

InChI Identifier

InChI=1S/C26H38O11/c1-12(27)36-17-10-15(21(31)33-4)24(2)8-7-14-16(28)9-13(11-25(14,3)19(24)18(17)29)26(32)20(30)22(34-5)37-23(26)35-6/h13-15,17,19-20,22-23,30,32H,7-11H2,1-6H3/t13-,14-,15-,17-,19-,20+,22+,23-,24-,25-,26+/m0/s1

InChI Key

ODBHOLKTMJCQDG-RRQPKOPKSA-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
Salvia divinorum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as colensane and clerodane diterpenoids. These are diterpenoids with a structure based on the clerodane or the colensane skeleton. Clerodanes arise from labdanes by two methyl migrations.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Colensane and clerodane diterpenoids

Alternative Parents

Substituents

Clerodane diterpenoid
Hydrophenanthrene
Phenanthrene
Glycosyl compound
O-glycosyl compound
Pentose monosaccharide
Alpha-acyloxy ketone
Dicarboxylic acid or derivatives
Monosaccharide
Methyl ester
Tetrahydrofuran
Tertiary alcohol
1,2-diol
Carboxylic acid ester
Ketone
Secondary alcohol
Acetal
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
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	0.9	ALOGPS
logP	0.98	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	11.66	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	154.89 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	125.1 m³·mol⁻¹	ChemAxon
Polarizability	54.92 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

28942452

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71454521

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate (NP0170050)

MOL for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

3D MOL for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

3D SDF for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

3D-SDF for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

PDB for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

3D PDB for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

SMILES for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

INCHI for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

Structure for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)

3D Structure for NP0170050 (methyl (1r,3s,4ar,4bs,6r,8ar,10ar)-3-(acetyloxy)-6-[(2s,3r,4s,5r)-3,4-dihydroxy-2,5-dimethoxyoxolan-3-yl]-4b,10a-dimethyl-4,8-dioxo-decahydrophenanthrene-1-carboxylate)