NP-MRD: Showing NP-Card for 12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid (NP0198162)

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Record Information

Version

2.0

Created at

2022-09-04 16:33:54 UTC

Updated at

2022-09-04 16:33:54 UTC

NP-MRD ID

NP0198162

Secondary Accession Numbers

None

Natural Product Identification

Common Name

12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid

Description

12-(5-Hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid 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. 12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid is found in Morus alba. 12-(5-Hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171504432D          

 34 35  0  0  0  0            999 V2000
   -0.5721   -5.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0515   -6.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4547   -6.3300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6374   -6.3300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2611   -6.8700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.1857   -6.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   10.3416   -9.3004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8840   -7.1401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  9 10  1  0  0  0  0
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  4 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END

     RDKit          3D

 79 80  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1533004171504432D          

 34 35  0  0  0  0            999 V2000
   -0.5721   -5.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0515   -6.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 20 29  1  0  0  0  0
 29 30  1  0  0  0  0
  4 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
  2 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0198162

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1NC(CCCCCCCCCC(CC(O)=O)OC2OC(CO)C(O)C(O)C2O)CCC1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H45NO9/c1-15-18(27)12-11-16(25-15)9-7-5-3-2-4-6-8-10-17(13-20(28)29)33-24-23(32)22(31)21(30)19(14-26)34-24/h15-19,21-27,30-32H,2-14H2,1H3,(H,28,29)

> <INCHI_KEY>
TYCHJCWFXCTGEJ-UHFFFAOYSA-N

> <FORMULA>
C24H45NO9

> <MOLECULAR_WEIGHT>
491.622

> <EXACT_MASS>
491.309432033

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
55.15782009242035

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid

> <ALOGPS_LOGP>
1.15

> <JCHEM_LOGP>
-1.4099883890608171

> <ALOGPS_LOGS>
-2.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.211662323527005

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9273652603278277

> <JCHEM_PKA_STRONGEST_BASIC>
10.063886839072788

> <JCHEM_POLAR_SURFACE_AREA>
168.94

> <JCHEM_REFRACTIVITY>
123.16269999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -1.068 -10.304   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.096 -11.312   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.551 -10.808   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.715 -11.816   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.171 -11.312   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.790 -11.816   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.954 -12.824   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.409 -12.320   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.573 -13.328   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.028 -12.824   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.193 -13.832   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.648 -13.328   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.812 -14.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.267 -13.832   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.558 -12.320   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      16.394 -11.312   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      19.013 -11.816   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      15.521 -15.849   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      16.685 -16.857   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      18.140 -16.353   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      19.304 -17.361   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      20.759 -16.857   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      21.924 -17.865   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      19.013 -18.873   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      20.177 -19.881   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      17.558 -19.377   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      17.267 -20.889   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      16.394 -18.369   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      14.939 -18.873   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       2.424 -13.328   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.969 -13.832   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.195 -12.824   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.650 -13.328   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   31                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   14   20                                                       
CONECT   20   19   21   29                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   20   30                                                  
CONECT   30   29                                                            
CONECT   31    4   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32    2   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Value	Source
12-(5-Hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoate	Generator

Chemical Formula

C₂₄H₄₅NO₉

Average Mass

491.6220 Da

Monoisotopic Mass

491.30943 Da

IUPAC Name

12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid

Traditional Name

12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid

CAS Registry Number

Not Available

SMILES

CC1NC(CCCCCCCCCC(CC(O)=O)OC2OC(CO)C(O)C(O)C2O)CCC1O

InChI Identifier

InChI=1S/C24H45NO9/c1-15-18(27)12-11-16(25-15)9-7-5-3-2-4-6-8-10-17(13-20(28)29)33-24-23(32)22(31)21(30)19(14-26)34-24/h15-19,21-27,30-32H,2-14H2,1H3,(H,28,29)

InChI Key

TYCHJCWFXCTGEJ-UHFFFAOYSA-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
Morus alba	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
Long-chain fatty acid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Alkaloid or derivatives
Amino fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Sugar acid
Oxane
Piperidine
Fatty acid
Monosaccharide
Secondary alcohol
Amino acid
Amino acid or derivatives
1,2-aminoalcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Oxacycle
Azacycle
Organoheterocyclic compound
Secondary amine
Monocarboxylic acid or derivatives
Polyol
Organic oxide
Hydrocarbon derivative
Amine
Organic oxygen compound
Organopnictogen compound
Carbonyl group
Organic nitrogen compound
Primary alcohol
Alcohol
Organonitrogen compound
Organooxygen compound
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	1.15	ALOGPS
logP	-1.4	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	3.93	ChemAxon
pKa (Strongest Basic)	10.06	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	168.94 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	123.16 m³·mol⁻¹	ChemAxon
Polarizability	55.16 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	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

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

73113475

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid (NP0198162)

MOL for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

3D MOL for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

3D SDF for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

3D-SDF for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

PDB for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

3D PDB for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

SMILES for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

INCHI for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

Structure for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)

3D Structure for NP0198162 (12-(5-hydroxy-6-methylpiperidin-2-yl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}dodecanoic acid)