NP-MRD: Showing NP-Card for 5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid (NP0321273)

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Record Information

Version

2.0

Created at

2022-09-11 23:23:59 UTC

Updated at

2022-09-11 23:23:59 UTC

NP-MRD ID

NP0321273

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid

Description

Simpotentin belongs to the class of organic compounds known as rhamnolipids. These are glycolipids structurally characterized by a glycosyl head group, in this case a rhamnose moiety, and a 3-(hydroxyalkanoyloxy)alkanoic acid (HAA) fatty acid tail. 5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid is found in Simplicillium minatense. 5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid was first documented in 2019 (PMID: 31246478). Based on a literature review very few articles have been published on Simpotentin (PMID: 30532035).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122201242D          

 36 36  0  0  1  0            999 V2000
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   -1.1171   -0.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  6 25  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309122201242D          

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    3.0925   -0.8399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7161   -1.3800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5602   -2.1901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4957   -1.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1193   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8988   -1.3800    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
  5  6  1  0  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  2  0  0  0  0
 10 12  1  0  0  0  0
  8 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  6  0  0  0
  6 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0321273

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC(CC(CC(O)=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)OC(=O)CC(O)CC(O)CCC

> <INCHI_IDENTIFIER>
InChI=1S/C24H44O12/c1-3-5-6-8-16(34-20(30)10-15(27)9-14(26)7-4-2)11-17(12-19(28)29)35-24-23(33)22(32)21(31)18(13-25)36-24/h14-18,21-27,31-33H,3-13H2,1-2H3,(H,28,29)/t14?,15?,16?,17?,18-,21-,22+,23+,24-/m1/s1

> <INCHI_KEY>
XUCHWPPLGKJKEI-IUJKDJJESA-N

> <FORMULA>
C24H44O12

> <MOLECULAR_WEIGHT>
524.604

> <EXACT_MASS>
524.283276857

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
54.26472715763027

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid

> <JCHEM_LOGP>
-0.19780747566666684

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.209274629940264

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.978566374661145

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7210062770069063

> <JCHEM_POLAR_SURFACE_AREA>
203.43999999999994

> <JCHEM_REFRACTIVITY>
124.95709999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
19

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       0.534  -7.617   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.825  -6.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.339  -5.096   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.048  -3.584   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.212  -2.576   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.921  -1.064   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.085  -0.056   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.540  -0.560   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.831  -2.072   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.194  -3.528   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.958  -4.592   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.705   0.449   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -6.160  -0.056   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -6.451  -1.568   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -7.906  -2.072   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.197  -3.584   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -9.652  -4.088   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -9.070  -1.064   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0     -10.525  -1.568   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -8.779   0.449   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -9.943   1.457   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -7.324   0.953   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -7.033   2.465   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.534  -0.560   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.698  -1.568   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.407  -3.080   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.153  -1.064   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.317  -2.072   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.026  -3.584   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.773  -1.568   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.937  -2.576   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.646  -4.088   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       8.392  -2.072   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.556  -3.080   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      11.011  -2.576   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    8   14                                                       
CONECT   14   13   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   14   24                                                  
CONECT   24   23                                                            
CONECT   25    6   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₄₄O₁₂

Average Mass

524.6040 Da

Monoisotopic Mass

524.28328 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CCCCCC(CC(CC(O)=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O)OC(=O)CC(O)CC(O)CCC

InChI Identifier

InChI=1S/C24H44O12/c1-3-5-6-8-16(34-20(30)10-15(27)9-14(26)7-4-2)11-17(12-19(28)29)35-24-23(33)22(32)21(31)18(13-25)36-24/h14-18,21-27,31-33H,3-13H2,1-2H3,(H,28,29)/t14?,15?,16?,17?,18-,21-,22+,23+,24-/m1/s1

InChI Key

XUCHWPPLGKJKEI-IUJKDJJESA-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
Simplicillium minatense	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as rhamnolipids. These are glycolipids structurally characterized by a glycosyl head group, in this case a rhamnose moiety, and a 3-(hydroxyalkanoyloxy)alkanoic acid (HAA) fatty acid tail.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Rhamnolipids

Alternative Parents

Substituents

Mono-rhamnolipid
Rhamnolipid
Fatty acyl glycoside of mono- or disaccharide
O-glycosyl compound
Glycosyl compound
Medium-chain fatty acid
Sugar acid
Hydroxy fatty acid
Heterocyclic fatty acid
Fatty acid ester
Beta-hydroxy acid
Oxane
Monosaccharide
Hydroxy acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
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

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

145720679

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ohtawa M, Shimizu E, Saito A, Sakamoto S, Waki A, Kondo A, Yagi A, Uchida R, Tomoda H, Nagamitsu T: Total Synthesis and Absolute Configuration of Simpotentin, a Potentiator of Amphotericin B Activity. Org Lett. 2019 Jul 19;21(14):5596-5599. doi: 10.1021/acs.orglett.9b01945. Epub 2019 Jun 27. [PubMed:31246478 ]
Uchida R, Kondo A, Yagi A, Nonaka K, Masuma R, Kobayashi K, Tomoda H: Simpotentin, a new potentiator of amphotericin B activity against Candida albicans, produced by Simplicillium minatense FKI-4981. J Antibiot (Tokyo). 2019 Mar;72(3):134-140. doi: 10.1038/s41429-018-0128-x. Epub 2018 Dec 10. [PubMed:30532035 ]
LOTUS database [Link]

Showing NP-Card for 5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid (NP0321273)

MOL for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

3D MOL for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

3D SDF for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

3D-SDF for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

PDB for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

3D PDB for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

SMILES for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

INCHI for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

Structure for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)

3D Structure for NP0321273 (5-[(3,5-dihydroxyoctanoyl)oxy]-3-{[(2r,3s,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}decanoic acid)