NP-MRD: Showing NP-Card for LysoSM(d18:0) (NP0091898)

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Record Information

Version

2.0

Created at

2022-05-11 18:51:25 UTC

Updated at

2022-05-11 18:51:25 UTC

NP-MRD ID

NP0091898

Secondary Accession Numbers

None

Natural Product Identification

Common Name

LysoSM(d18:0)

Description

LysoSM(d18:0), Also known as SM(D18:0/0:0) Or lysosphingomyelin, belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group. Thus, lysosm(D18:0) Is considered to be a sphingoid base lipid molecule. LysoSM(d18:0) is found in Trypanosoma brucei. LysoSM(d18:0) Is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241203382D          

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M  CHG  2  25   1  27  -1
M  END

     RDKit          3D

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M  CHG  2  24  -1  28   1
M  END


  Mrv0541 02241203382D          

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 29 31  1  0  0  0  0
 30 31  1  0  0  0  0
M  CHG  2  25   1  27  -1
M  END
> <DATABASE_ID>
NP0091898

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCCCCCC[C@@H](O)[C@@H](N)COP([O-])(=O)OCC[N+](C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C23H51N2O5P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(26)22(24)21-30-31(27,28)29-20-19-25(2,3)4/h22-23,26H,5-21,24H2,1-4H3/t22-,23+/m0/s1

> <INCHI_KEY>
GSEOJHIBPQRSNH-XZOQPEGZSA-N

> <FORMULA>
C23H51N2O5P

> <MOLECULAR_WEIGHT>
466.6352

> <EXACT_MASS>
466.353559264

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
56.39202063239314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium

> <ALOGPS_LOGP>
1.72

> <JCHEM_LOGP>
-0.047308685495615635

> <ALOGPS_LOGS>
-5.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.537794180548442

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8298530348162707

> <JCHEM_PKA_STRONGEST_BASIC>
9.732916580907874

> <JCHEM_POLAR_SURFACE_AREA>
104.84

> <JCHEM_REFRACTIVITY>
139.0956

> <JCHEM_ROTATABLE_BOND_COUNT>
22

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.04e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      33.262 -19.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.385 -11.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.465 -11.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.925 -10.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.929 -18.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      30.595 -19.550   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      29.261 -18.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      27.927 -19.550   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      26.594 -18.780   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      25.260 -19.550   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.926 -18.780   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      22.593 -19.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.259 -18.780   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      19.925 -19.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      18.592 -18.780   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.258 -19.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.924 -18.780   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.591 -19.550   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      19.925 -13.390   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      18.592 -14.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.591 -16.470   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.257 -17.240   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.257 -18.780   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      11.473 -16.970   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      19.925 -11.850   0.000  0.00  0.00           N+1
HETATM   26  O   UNK     0      11.923 -19.550   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      16.488 -15.136   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0      18.028 -17.803   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      18.592 -15.700   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      15.924 -17.240   0.000  0.00  0.00           O+0
HETATM   31  P   UNK     0      17.258 -16.470   0.000  0.00  0.00           P+0
CONECT    1    5                                                            
CONECT    2   25                                                            
CONECT    3   25                                                            
CONECT    4   25                                                            
CONECT    5    1    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                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   23                                                       
CONECT   19   20   25                                                       
CONECT   20   19   29                                                       
CONECT   21   22   30                                                       
CONECT   22   21   23   24                                                  
CONECT   23   18   22   26                                                  
CONECT   24   22                                                            
CONECT   25    2    3    4   19                                             
CONECT   26   23                                                            
CONECT   27   31                                                            
CONECT   28   31                                                            
CONECT   29   20   31                                                       
CONECT   30   21   31                                                       
CONECT   31   27   28   29   30                                             
MASTER        0    0    0    0    0    0    0    0   31    0   60    0
END

View in JSmol

Synonyms

Value	Source
Dihydrosphingosine-1-phosphocholine	ChEBI
Dihydrosphingosylphosphorylcholine	ChEBI
SM(D18:0/0:0)	ChEBI
Lysosphingomyelin	HMDB
Sphinganine-1-phosphocholine	HMDB
Sphingomyelin(D18:0/0:0)	HMDB
LysoSM(D18:0)	ChEBI

Chemical Formula

C₂₃H₅₁N₂O₅P

Average Mass

466.6352 Da

Monoisotopic Mass

466.35356 Da

IUPAC Name

(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium

Traditional Name

(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCCCCCC[C@@H](O)[C@@H](N)COP([O-])(=O)OCC[N+](C)(C)C

InChI Identifier

InChI=1S/C23H51N2O5P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(26)22(24)21-30-31(27,28)29-20-19-25(2,3)4/h22-23,26H,5-21,24H2,1-4H3/t22-,23+/m0/s1

InChI Key

GSEOJHIBPQRSNH-XZOQPEGZSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Phosphosphingolipids

Direct Parent

Phosphosphingolipids

Alternative Parents

Substituents

Sphingoid-1-phosphate or derivatives
Phosphocholine
Phosphoethanolamine
Dialkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetraalkylammonium salt
Quaternary ammonium salt
1,2-aminoalcohol
Secondary alcohol
Organic nitrogen compound
Organic zwitterion
Organic salt
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Primary aliphatic amine
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Lysosphingomyelins and lysoglycosphingolipids (LMSP01060002 )

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	1.72	ALOGPS
logP	-0.047	ChemAxon
logS	-5.9	ALOGPS
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	9.73	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	104.84 Å²	ChemAxon
Rotatable Bond Count	22	ChemAxon
Refractivity	139.1 m³·mol⁻¹	ChemAxon
Polarizability	56.39 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0012082

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB028751

KNApSAcK ID

Not Available

Chemspider ID

21403135

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44260122

PDB ID

Not Available

ChEBI ID

132478

Good Scents ID

Not Available

References

General References

Showing NP-Card for LysoSM(d18:0) (NP0091898)

MOL for NP0091898 (LysoSM(d18:0))

3D MOL for NP0091898 (LysoSM(d18:0))

3D SDF for NP0091898 (LysoSM(d18:0))

3D-SDF for NP0091898 (LysoSM(d18:0))

PDB for NP0091898 (LysoSM(d18:0))

3D PDB for NP0091898 (LysoSM(d18:0))

SMILES for NP0091898 (LysoSM(d18:0))

INCHI for NP0091898 (LysoSM(d18:0))

Structure for NP0091898 (LysoSM(d18:0))

3D Structure for NP0091898 (LysoSM(d18:0))