NP-MRD: Showing NP-Card for 10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid (NP0153777)

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Record Information

Version

2.0

Created at

2022-09-02 10:29:55 UTC

Updated at

2022-09-02 10:29:56 UTC

NP-MRD ID

NP0153777

Secondary Accession Numbers

None

Natural Product Identification

Common Name

10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid

Description

10-(2-Decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.G. S-,C-, or N-type) has been reported. 10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid is found in Plakortis simplex. 10-(2-Decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241502272D          

 69 71  0  0  0  0            999 V2000
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M  END


  Mrv1533004241502272D          

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 41 42  1  0  0  0  0
 41 43  1  0  0  0  0
 25 44  1  0  0  0  0
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M  END
> <DATABASE_ID>
NP0153777

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCC1CC1CCCCC=CCCCC(O)C(COC1OC(CO)C(O)C(O)C1OCC=C(C)C)NC(=O)C(O)CCC=CCCCCC1CC1CCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C59H107NO9/c1-5-7-9-11-13-16-22-28-34-47-42-49(47)36-30-24-18-15-19-26-32-38-52(62)51(45-68-59-57(67-41-40-46(3)4)56(65)55(64)54(44-61)69-59)60-58(66)53(63)39-33-27-21-20-25-31-37-50-43-48(50)35-29-23-17-14-12-10-8-6-2/h15,19,21,27,40,47-57,59,61-65H,5-14,16-18,20,22-26,28-39,41-45H2,1-4H3,(H,60,66)

> <INCHI_KEY>
VXRKQDJTQHPQIU-UHFFFAOYSA-N

> <FORMULA>
C59H107NO9

> <MOLECULAR_WEIGHT>
974.503

> <EXACT_MASS>
973.794584029

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
176

> <JCHEM_AVERAGE_POLARIZABILITY>
122.52638091285162

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
10-(2-decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enamide

> <ALOGPS_LOGP>
9.29

> <JCHEM_LOGP>
14.376308284

> <ALOGPS_LOGS>
-6.77

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.922135170317674

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.358657731667513

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083626267373

> <JCHEM_POLAR_SURFACE_AREA>
157.94

> <JCHEM_REFRACTIVITY>
285.4212000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
45

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.64e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
10-(2-decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
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HETATM   24  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
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HETATM   38  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
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HETATM   40  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
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HETATM   44  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
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HETATM   47  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      16.004  -4.620   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      17.338  -5.390   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      18.672  -4.620   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      19.442  -3.286   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      20.212  -4.620   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      21.545  -5.390   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      22.879  -4.620   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      24.213  -5.390   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      25.546  -4.620   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      26.880  -5.390   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      28.214  -4.620   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      29.547  -5.390   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      30.881  -4.620   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      32.215  -5.390   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      33.548  -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                                                       
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   13                                                  
CONECT   12   11   13                                                       
CONECT   13   12   11   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   44                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   37                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   33                                                  
CONECT   31   30   32                                                       
CONECT   32   31                                                            
CONECT   33   30   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   28   38                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41                                                            
CONECT   44   25   45                                                       
CONECT   45   44   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   48   49                                                  
CONECT   48   47                                                            
CONECT   49   47   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57   59                                                       
CONECT   59   58   57   60                                                  
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  142    0
END

View in JSmol

Synonyms

Value	Source
10-(2-Decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidate	Generator

Chemical Formula

C₅₉H₁₀₇NO₉

Average Mass

974.5030 Da

Monoisotopic Mass

973.79458 Da

IUPAC Name

10-(2-decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enamide

Traditional Name

10-(2-decylcyclopropyl)-N-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enamide

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCC1CC1CCCCC=CCCCC(O)C(COC1OC(CO)C(O)C(O)C1OCC=C(C)C)NC(=O)C(O)CCC=CCCCCC1CC1CCCCCCCCCC

InChI Identifier

InChI=1S/C59H107NO9/c1-5-7-9-11-13-16-22-28-34-47-42-49(47)36-30-24-18-15-19-26-32-38-52(62)51(45-68-59-57(67-41-40-46(3)4)56(65)55(64)54(44-61)69-59)60-58(66)53(63)39-33-27-21-20-25-31-37-50-43-48(50)35-29-23-17-14-12-10-8-6-2/h15,19,21,27,40,47-57,59,61-65H,5-14,16-18,20,22-26,28-39,41-45H2,1-4H3,(H,60,66)

InChI Key

VXRKQDJTQHPQIU-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Plakortis simplex	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.G. S-,C-, or N-type) has been reported.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Glycosphingolipids

Direct Parent

Glycosphingolipids

Alternative Parents

Substituents

Glycosphingolipid
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Fatty acyl
Fatty amide
Monosaccharide
Oxane
N-acyl-amine
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Dialkyl ether
Ether
Acetal
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Organonitrogen 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	9.29	ALOGPS
logP	14.38	ChemAxon
logS	-6.8	ALOGPS
pKa (Strongest Acidic)	12.36	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	157.94 Å²	ChemAxon
Rotatable Bond Count	45	ChemAxon
Refractivity	285.42 m³·mol⁻¹	ChemAxon
Polarizability	122.53 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid (NP0153777)

MOL for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

3D MOL for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

3D SDF for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

3D-SDF for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

PDB for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

3D PDB for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

SMILES for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

INCHI for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

Structure for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)

3D Structure for NP0153777 (10-(2-decylcyclopropyl)-n-[12-(2-decylcyclopropyl)-1-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3-methylbut-2-en-1-yl)oxy]oxan-2-yl]oxy}-3-hydroxydodec-7-en-2-yl]-2-hydroxydec-5-enimidic acid)