NP-MRD: Showing NP-Card for psychosine (NP0271317)

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Record Information

Version

2.0

Created at

2022-09-08 17:34:17 UTC

Updated at

2022-09-08 17:34:18 UTC

NP-MRD ID

NP0271317

Secondary Accession Numbers

None

Natural Product Identification

Common Name

psychosine

Description

Galactosylsphingosine, also known as beta-psychosine or sphingosine galactoside, 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. Galactosylsphingosine is a very strong basic compound (based on its pKa). psychosine was first documented in 1984 (PMID: 6719111). A glycosylsphingoid consisting of sphingosine having a beta-D-galactosyl residue attached at the 1-position (PMID: 3585345) (PMID: 2465381) (PMID: 8069245) (PMID: 3239954).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306041822512D          

 32 32  0  0  1  0            999 V2000
   12.7132  -21.6290    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9939  -21.2212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7132  -22.4581    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.4232  -21.2212    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   11.9939  -22.8659    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   11.9939  -23.6861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652306041822512D          

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   12.7132  -21.6290    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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 26 29  1  0  0  0  0
 29 30  1  0  0  0  0
 24 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0271317

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H47NO7/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)18(25)17-31-24-23(30)22(29)21(28)20(16-26)32-24/h14-15,18-24,26-30H,2-13,16-17,25H2,1H3/b15-14+/t18-,19+,20+,21-,22-,23+,24+/m0/s1

> <INCHI_KEY>
HHJTWTPUPVQKNA-PIIMIWFASA-N

> <FORMULA>
C24H47NO7

> <MOLECULAR_WEIGHT>
461.64

> <EXACT_MASS>
461.335252857

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.48377702857766

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R,6R)-2-{[(4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
3.16

> <JCHEM_LOGP>
2.795744402999998

> <ALOGPS_LOGS>
-3.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.16092564682734

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.20649866259466

> <JCHEM_PKA_STRONGEST_BASIC>
9.12180575925232

> <JCHEM_POLAR_SURFACE_AREA>
145.63

> <JCHEM_REFRACTIVITY>
124.30529999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.04e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R,6R)-2-{[(4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-18         0                                  
HETATM    1  C   UNK     0      23.731 -40.374   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      22.389 -39.613   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      23.731 -41.922   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      25.057 -39.613   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      21.055 -40.374   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.389 -42.683   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      25.057 -42.683   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      26.400 -40.370   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.055 -41.922   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.738 -39.613   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      22.389 -44.214   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      27.719 -39.588   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      19.738 -42.683   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      29.060 -40.346   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      27.705 -38.049   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      30.387 -39.564   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      29.074 -41.876   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      31.720 -40.321   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      33.047 -39.539   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      34.379 -40.297   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      35.706 -39.515   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      37.039 -40.272   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      38.366 -39.490   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      39.707 -40.248   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      18.404 -40.371   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      34.390 -41.829   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      33.068 -42.605   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      31.735 -41.847   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      35.729 -42.591   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      37.051 -41.813   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      39.723 -41.788   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      38.391 -42.572   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1    8                                                       
CONECT    5    2    9   10                                                  
CONECT    6    3   11    9                                                  
CONECT    7    3                                                            
CONECT    8    4   12                                                       
CONECT    9    5   13    6                                                  
CONECT   10    5   25                                                       
CONECT   11    6                                                            
CONECT   12    8   14   15                                                  
CONECT   13    9                                                            
CONECT   14   12   16   17                                                  
CONECT   15   12                                                            
CONECT   16   14   18                                                       
CONECT   17   14                                                            
CONECT   18   16   19                                                       
CONECT   19   20   18                                                       
CONECT   20   21   19                                                       
CONECT   21   22   20                                                       
CONECT   22   23   21                                                       
CONECT   23   22   24                                                       
CONECT   24   23   31                                                       
CONECT   25   10                                                            
CONECT   26   27   29                                                       
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26   30                                                       
CONECT   30   29   32                                                       
CONECT   31   24   32                                                       
CONECT   32   30   31                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   64    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,4E)-2-Amino-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-ene	ChEBI
1-beta-D-Galactosphingosine	ChEBI
1-beta-D-Galactosylsphingosine	ChEBI
1-O-beta-D-Galactopyranosylsphingosine	ChEBI
1-O-beta-D-Galactosylsphingosine	ChEBI
beta-Psychosine	ChEBI
O-Galactosylsphingosine	ChEBI
Sphingosine galactoside	ChEBI
(2S,3R,4E)-2-Amino-1-(b-D-galactopyranosyloxy)-3-hydroxyoctadec-4-ene	Generator
(2S,3R,4E)-2-Amino-1-(β-D-galactopyranosyloxy)-3-hydroxyoctadec-4-ene	Generator
1-b-D-Galactosphingosine	Generator
1-b-D-Galactosylsphingosine	Generator
1-O-b-D-Galactopyranosylsphingosine	Generator
1-O-b-D-Galactosylsphingosine	Generator
b-Psychosine	Generator
Galactoside, sphingosine	HMDB
Psychosine	HMDB
Erythro-psychosine	HMDB
Galactosylsphingosine	ChEBI

Chemical Formula

C₂₄H₄₇NO₇

Average Mass

461.6400 Da

Monoisotopic Mass

461.33525 Da

IUPAC Name

(2R,3R,4S,5R,6R)-2-{[(4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,4S,5R,6R)-2-{[(4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)CO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C24H47NO7/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)18(25)17-31-24-23(30)22(29)21(28)20(16-26)32-24/h14-15,18-24,26-30H,2-13,16-17,25H2,1H3/b15-14+/t18-,19+,20+,21-,22-,23+,24+/m0/s1

InChI Key

HHJTWTPUPVQKNA-PIIMIWFASA-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

Not Available

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
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Fatty acyl
Oxane
Monosaccharide
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Acetal
Polyol
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Primary aliphatic amine
Primary alcohol
Primary amine
Alcohol
Organic nitrogen compound
Amine
Hydrocarbon derivative
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glycosylsphingoid (CHEBI:16874 )
Sphingoid base analogs (C01747 )
Basic glycosphingolipids (C01747 )

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	3.16	ALOGPS
logP	2.8	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	9.12	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	145.63 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	124.31 m³·mol⁻¹	ChemAxon
Polarizability	54.48 Å³	ChemAxon
Number of Rings	1	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

HMDB0000648

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022161

KNApSAcK ID

Not Available

Chemspider ID

4444111

KEGG Compound ID

C01747

BioCyc ID

PSYCHOSINE

BiGG ID

Not Available

Wikipedia Link

Psychosine

METLIN ID

5620

PubChem Compound

5280458

PDB ID

Not Available

ChEBI ID

16874

Good Scents ID

Not Available

References

General References

Shinoda H, Kobayashi T, Katayama M, Goto I, Nagara H: Accumulation of galactosylsphingosine (psychosine) in the twitcher mouse: determination by HPLC. J Neurochem. 1987 Jul;49(1):92-9. doi: 10.1111/j.1471-4159.1987.tb03399.x. [PubMed:3585345 ]
Yoshimura T, Kobayashi T, Mitsuo K, Goto I: Decreased fatty acylation of myelin proteolipid protein in the twitcher mouse. J Neurochem. 1989 Mar;52(3):836-41. doi: 10.1111/j.1471-4159.1989.tb02529.x. [PubMed:2465381 ]
Igisu H, Suzuki K: Progressive accumulation of toxic metabolite in a genetic leukodystrophy. Science. 1984 May 18;224(4650):753-5. doi: 10.1126/science.6719111. [PubMed:6719111 ]
Chiba M, Tsuchihashi K, Suetake K, Ibayashi Y, Gasa S, Hashi K: Photoaffinity labeling of lipoproteins in human cerebrospinal fluid with a heterobifunctional derivative of galactosylsphingosine. Biochem Mol Biol Int. 1994 Apr;32(5):961-71. [PubMed:8069245 ]
Kobayashi T, Goto I, Yamanaka T, Suzuki Y, Nakano T, Suzuki K: Infantile and fetal globoid cell leukodystrophy: analysis of galactosylceramide and galactosylsphingosine. Ann Neurol. 1988 Oct;24(4):517-22. doi: 10.1002/ana.410240407. [PubMed:3239954 ]
LOTUS database [Link]

Showing NP-Card for psychosine (NP0271317)

MOL for NP0271317 (psychosine)

3D MOL for NP0271317 (psychosine)

3D SDF for NP0271317 (psychosine)

3D-SDF for NP0271317 (psychosine)

PDB for NP0271317 (psychosine)

3D PDB for NP0271317 (psychosine)

SMILES for NP0271317 (psychosine)

INCHI for NP0271317 (psychosine)

Structure for NP0271317 (psychosine)

3D Structure for NP0271317 (psychosine)