NP-MRD: Showing NP-Card for (3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid (NP0321954)

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Record Information

Version

2.0

Created at

2022-09-12 00:26:32 UTC

Updated at

2022-09-12 00:26:32 UTC

NP-MRD ID

NP0321954

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid

Description

(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methyl-2H-chromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid belongs to the class of organic compounds known as saccharolipids. Saccharolipids are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety. (3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid is found in Ageratina altissima. Based on a literature review very few articles have been published on (3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methyl-2H-chromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122202262D          

 37 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309122202262D          

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  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 14 15  1  0  0  0  0
 16 15  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  6  0  0  0
 24 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 18 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 16 35  1  0  0  0  0
 35 36  1  1  0  0  0
 12 37  1  0  0  0  0
  7 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0321954

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)C1=CC=C2O[C@@](C)(CO[C@@H]3O[C@H](COC(=O)C[C@@](C)(O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]3O)C=CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O12/c1-13(26)14-4-5-16-15(8-14)6-7-25(3,37-16)12-35-23-22(32)21(31)20(30)17(36-23)11-34-19(29)10-24(2,33)9-18(27)28/h4-8,17,20-23,30-33H,9-12H2,1-3H3,(H,27,28)/t17-,20-,21+,22-,23-,24+,25-/m1/s1

> <INCHI_KEY>
KSRUZCVAFJSUFJ-RPIXIFGUSA-N

> <FORMULA>
C25H32O12

> <MOLECULAR_WEIGHT>
524.519

> <EXACT_MASS>
524.18937647

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
52.43971955135442

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methyl-2H-chromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid

> <JCHEM_LOGP>
-0.46999899199999856

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.211292843742347

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7531631510514303

> <JCHEM_PKA_STRONGEST_BASIC>
-3.008392090148276

> <JCHEM_POLAR_SURFACE_AREA>
189.27999999999997

> <JCHEM_REFRACTIVITY>
125.4567

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic 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      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.518  -2.043   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.528  -3.757   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.044  -4.025   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.571  -5.472   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.088  -5.739   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.614  -7.186   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.131  -7.454   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.658  -8.901   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.174  -9.168   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.164  -7.988   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      12.701 -10.615   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.218 -10.883   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.950 -12.399   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      14.485  -9.366   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      15.734 -11.150   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      16.261 -12.597   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      17.778 -12.865   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      15.271 -13.777   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       7.624  -8.366   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       8.151  -9.813   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.108  -8.099   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.118  -9.278   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       5.581  -6.651   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.065  -6.384   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   37                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   37                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   35                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   31                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   18   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   16   36                                                  
CONECT   36   35                                                            
CONECT   37   12    7                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Value	Source
(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methyl-2H-chromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoate	Generator

Chemical Formula

C₂₅H₃₂O₁₂

Average Mass

524.5190 Da

Monoisotopic Mass

524.18938 Da

IUPAC Name

(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methyl-2H-chromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid

Traditional Name

(3S)-5-{[(2R,3S,4S,5R,6R)-6-{[(2R)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid

CAS Registry Number

Not Available

SMILES

CC(=O)C1=CC=C2O[C@@](C)(CO[C@@H]3O[C@H](COC(=O)C[C@@](C)(O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]3O)C=CC2=C1

InChI Identifier

InChI=1S/C25H32O12/c1-13(26)14-4-5-16-15(8-14)6-7-25(3,37-16)12-35-23-22(32)21(31)20(30)17(36-23)11-34-19(29)10-24(2,33)9-18(27)28/h4-8,17,20-23,30-33H,9-12H2,1-3H3,(H,27,28)/t17-,20-,21+,22-,23-,24+,25-/m1/s1

InChI Key

KSRUZCVAFJSUFJ-RPIXIFGUSA-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
Eupatorium rugosum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as saccharolipids. Saccharolipids are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Saccharolipids

Sub Class

Not Available

Direct Parent

Saccharolipids

Alternative Parents

Substituents

Saccharolipid
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
Acetophenone
Aryl ketone
Aryl alkyl ketone
Alkyl aryl ether
Fatty acid ester
Dicarboxylic acid or derivatives
Benzenoid
Monosaccharide
Oxane
Fatty acyl
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Ketone
Oxacycle
Polyol
Acetal
Carboxylic acid derivative
Carboxylic acid
Organoheterocyclic compound
Ether
Organooxygen compound
Alcohol
Organic oxide
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	-0.47	ChemAxon
pKa (Strongest Acidic)	3.75	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	189.28 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	125.46 m³·mol⁻¹	ChemAxon
Polarizability	52.44 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	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

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

162983385

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid (NP0321954)

MOL for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

3D MOL for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

3D SDF for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

3D-SDF for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

PDB for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

3D PDB for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

SMILES for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

INCHI for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

Structure for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)

3D Structure for NP0321954 ((3s)-5-{[(2r,3s,4s,5r,6r)-6-{[(2r)-6-acetyl-2-methylchromen-2-yl]methoxy}-3,4,5-trihydroxyoxan-2-yl]methoxy}-3-hydroxy-3-methyl-5-oxopentanoic acid)