NP-MRD: Showing NP-Card for (6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one (NP0282033)

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Record Information

Version

2.0

Created at

2022-09-09 08:42:20 UTC

Updated at

2022-09-09 08:42:20 UTC

NP-MRD ID

NP0282033

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one

Description

Ratjadon belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. (6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one is found in Sorangium cellulosum. (6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one was first documented in 1995 (PMID: 7592065). Based on a literature review very few articles have been published on Ratjadon.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092210422D          

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M  END

     RDKit          3D

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  Mrv1652309092210422D          

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 26 28  1  0  0  0  0
 22 28  1  0  0  0  0
  6 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
  4 32  1  0  0  0  0
 32 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0282033

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C\[C@@H]1O[C@@H](C[C@@H](O)[C@@H]1C)[C@H](O)\C=C\C=C(/C)C[C@@H](C)\C=C(\C)/C=C/[C@H]1CC=CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O5/c1-6-9-26-22(5)25(30)18-27(33-26)24(29)12-7-10-19(2)16-21(4)17-20(3)14-15-23-11-8-13-28(31)32-23/h6-10,12-15,17,21-27,29-30H,11,16,18H2,1-5H3/b9-6+,12-7+,15-14+,19-10+,20-17-/t21-,22+,23-,24-,25-,26+,27+/m1/s1

> <INCHI_KEY>
CAYGMWMWJUFODP-AYFTZVAISA-N

> <FORMULA>
C28H40O5

> <MOLECULAR_WEIGHT>
456.623

> <EXACT_MASS>
456.287574388

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
52.14162774849306

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6R)-6-[(1E,3Z,5R,7E,9E,11R)-11-hydroxy-11-[(2S,4R,5S,6S)-4-hydroxy-5-methyl-6-[(1E)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydro-2H-pyran-2-one

> <JCHEM_LOGP>
5.014277186333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.827530891729761

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.76672919578849

> <JCHEM_PKA_STRONGEST_BASIC>
-2.896096966045338

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
138.5849

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(6R)-6-[(1E,3Z,5R,7E,9E,11R)-11-hydroxy-11-[(2S,4R,5S,6S)-4-hydroxy-5-methyl-6-[(1E)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -6.668   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.000  10.780   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   32                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   29                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   22                                                       
CONECT   29    6   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    4   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Value	Source
Ratjadone	MeSH
(+)-Ratjadone	MeSH
Ratjadone a	MeSH

Chemical Formula

C₂₈H₄₀O₅

Average Mass

456.6230 Da

Monoisotopic Mass

456.28757 Da

IUPAC Name

(6R)-6-[(1E,3Z,5R,7E,9E,11R)-11-hydroxy-11-[(2S,4R,5S,6S)-4-hydroxy-5-methyl-6-[(1E)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydro-2H-pyran-2-one

Traditional Name

(6R)-6-[(1E,3Z,5R,7E,9E,11R)-11-hydroxy-11-[(2S,4R,5S,6S)-4-hydroxy-5-methyl-6-[(1E)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one

CAS Registry Number

Not Available

SMILES

C\C=C\[C@@H]1O[C@@H](C[C@@H](O)[C@@H]1C)[C@H](O)\C=C\C=C(/C)C[C@@H](C)\C=C(\C)/C=C/[C@H]1CC=CC(=O)O1

InChI Identifier

InChI=1S/C28H40O5/c1-6-9-26-22(5)25(30)18-27(33-26)24(29)12-7-10-19(2)16-21(4)17-20(3)14-15-23-11-8-13-28(31)32-23/h6-10,12-15,17,21-27,29-30H,11,16,18H2,1-5H3/b9-6+,12-7+,15-14+,19-10+,20-17-/t21-,22+,23-,24-,25-,26+,27+/m1/s1

InChI Key

CAYGMWMWJUFODP-AYFTZVAISA-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
Sorangium cellulosum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Long chain fatty alcohol
Monocyclic monoterpenoid
Monoterpenoid
Fatty alcohol
Dihydropyranone
Fatty acyl
Pyran
Oxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Carboxylic acid ester
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Monocarboxylic acid or derivatives
Alcohol
Organic oxygen compound
Organooxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	5.01	ChemAxon
pKa (Strongest Acidic)	13.77	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	138.58 m³·mol⁻¹	ChemAxon
Polarizability	52.14 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00016579

Chemspider ID

4948244

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6444320

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gerth K, Schummer D, Hofle G, Irschik H, Reichenbach H: Ratjadon: a new antifungal compound from Sorangium cellulosum (myxobacteria) production, physio-chemical and biological properties. J Antibiot (Tokyo). 1995 Sep;48(9):973-6. doi: 10.7164/antibiotics.48.973. [PubMed:7592065 ]
LOTUS database [Link]

Showing NP-Card for (6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one (NP0282033)

MOL for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

3D MOL for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

3D SDF for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

3D-SDF for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

PDB for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

3D PDB for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

SMILES for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

INCHI for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

Structure for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)

3D Structure for NP0282033 ((6r)-6-[(1e,3z,5r,7e,9e,11r)-11-hydroxy-11-[(2s,4r,5s,6s)-4-hydroxy-5-methyl-6-[(1e)-prop-1-en-1-yl]oxan-2-yl]-3,5,7-trimethylundeca-1,3,7,9-tetraen-1-yl]-5,6-dihydropyran-2-one)