NP-MRD: Showing NP-Card for n,n-dimethylsphingosine (NP0225469)

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Record Information

Version

2.0

Created at

2022-09-06 04:11:53 UTC

Updated at

2022-09-06 04:11:54 UTC

NP-MRD ID

NP0225469

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n,n-dimethylsphingosine

Description

N,N-Dimethylsphingosine, also known as DMS or N,N-dimethylsphing-4-enine, belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom. Thus, N,N-dimethylsphingosine is considered to be a sphingoid base lipid molecule. N,N-Dimethylsphingosine induces apoptosis, but it is not an inhibitor of protein kinase C. N,N-Dimethylsphingosine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Other studies have indicated that N,N-Dimethylsphingosine inhibits airway inflammation in asthma (PMID: 18359884 ) And is cardioprotective (PMID: 16831409 ). N,N-Dimethylsphingosine induces apoptosis, but it is not an inhibitor of protein kinase C. N,N-Dimethylsphingosine (DMS) has recently been identified as an inducer of pain in a rat model of chronic pain. It has properties similar to capsaicin (PMID: 16740613 ). n,n-dimethylsphingosine is found in Trypanosoma brucei. n,n-dimethylsphingosine was first documented in 2006 (PMID: 16740613). It is a natural metabolite of sphingosine in some cancer cell lines and tissues (PMID: 22267119) (PMID: 18359884) (PMID: 16831409).

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 02271200292D          

 23 22  0  0  1  0            999 V2000
    6.1756   -4.5913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8901   -4.1788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6046   -4.5913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3191   -4.1788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1756   -5.4163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8901   -5.8288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6046   -5.4163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3191   -5.8288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0335   -5.4163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7480   -5.8288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4625   -5.4163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1770   -5.8289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8915   -5.4164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6059   -5.8289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3204   -5.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0349   -5.8290    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.7494   -5.4165    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.0349   -6.6540    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4638   -5.8290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7494   -4.5915    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.4639   -4.1790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0349   -4.1789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1783   -5.4166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 14  2  0  0  0  0
 16 15  1  0  0  0  0
 17 16  1  0  0  0  0
 16 18  1  6  0  0  0
 19 17  1  0  0  0  0
 17 20  1  1  0  0  0
 21 20  1  0  0  0  0
 22 20  1  0  0  0  0
 23 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0225469

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H41NO2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-20(23)19(18-22)21(2)3/h16-17,19-20,22-23H,4-15,18H2,1-3H3/b17-16+/t19-,20+/m0/s1

> <INCHI_KEY>
YRXOQXUDKDCXME-YIVRLKKSSA-N

> <FORMULA>
C20H41NO2

> <MOLECULAR_WEIGHT>
327.545

> <EXACT_MASS>
327.313729561

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
43.619629102598935

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,4E)-2-(dimethylamino)octadec-4-ene-1,3-diol

> <ALOGPS_LOGP>
5.33

> <JCHEM_LOGP>
5.382208379666666

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.17615004683628

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.102716919598699

> <JCHEM_PKA_STRONGEST_BASIC>
8.908557139625296

> <JCHEM_POLAR_SURFACE_AREA>
43.7

> <JCHEM_REFRACTIVITY>
101.96129999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.73e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N,N-dimethylsphingosine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1  C   UNK     0      11.528  -8.570   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.862  -7.800   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.195  -8.570   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.529  -7.800   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.528 -10.110   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.862 -10.880   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.195 -10.110   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.529 -10.880   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.863 -10.110   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.196 -10.880   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.530 -10.110   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.864 -10.881   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.197 -10.111   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      23.531 -10.881   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      24.865 -10.111   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      26.198 -10.881   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      27.532 -10.111   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      26.198 -12.421   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      28.866 -10.881   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      27.532  -8.571   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      28.866  -7.801   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      26.198  -7.801   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      30.199 -10.111   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
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   18                                                  
CONECT   17   16   19   20                                                  
CONECT   18   16                                                            
CONECT   19   17   23                                                       
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   19                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   44    0
END

View in JSmol

Synonyms

Value	Source
N,N-Dimethyl-D-erythro-sphingosine	ChEBI
N,N-Dimethylsphing-4-enine	ChEBI
(S-(R,S-(e)))-2-(Dimethylamino)-4-octadecene-1,3-diol	HMDB
DMS	HMDB
N,N-Dimethyl-D-erythro-sphingosine]	HMDB
N,N-Dimethyl-erythro-sphingosine	HMDB
N,N-DMS	HMDB
D-Erythro-N,N-dimethylsphingosine	HMDB
DMS CPD	HMDB
(2R,3S,e)-2-(Dimethylamino)octadec-4-ene-1,3-diol	MeSH

Chemical Formula

C₂₀H₄₁NO₂

Average Mass

327.5450 Da

Monoisotopic Mass

327.31373 Da

IUPAC Name

(2S,3R,4E)-2-(dimethylamino)octadec-4-ene-1,3-diol

Traditional Name

N,N-dimethylsphingosine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C20H41NO2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-20(23)19(18-22)21(2)3/h16-17,19-20,22-23H,4-15,18H2,1-3H3/b17-16+/t19-,20+/m0/s1

InChI Key

YRXOQXUDKDCXME-YIVRLKKSSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,2-aminoalcohols

Alternative Parents

Substituents

Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
1,2-aminoalcohol
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tertiary amino compound (CHEBI:78759 )
sphingoid (CHEBI:78759 )
aminodiol (CHEBI:78759 )
N-methylated sphingoid bases (C13914 )
N-methylated sphingoid bases (LMSP01070001 )

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	5.33	ALOGPS
logP	5.38	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	14.1	ChemAxon
pKa (Strongest Basic)	8.91	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	43.7 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	101.96 m³·mol⁻¹	ChemAxon
Polarizability	43.62 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0013645

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029615

KNApSAcK ID

Not Available

Chemspider ID

4445480

KEGG Compound ID

C13914

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

N,N-Dimethylsphingosine

METLIN ID

Not Available

PubChem Compound

5282309

PDB ID

Not Available

ChEBI ID

78759

Good Scents ID

Not Available

References

General References

Patti GJ, Yanes O, Shriver LP, Courade JP, Tautenhahn R, Manchester M, Siuzdak G: Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin. Nat Chem Biol. 2012 Jan 22;8(3):232-4. doi: 10.1038/nchembio.767. [PubMed:22267119 ]
Zhang YH, Vasko MR, Nicol GD: Intracellular sphingosine 1-phosphate mediates the increased excitability produced by nerve growth factor in rat sensory neurons. J Physiol. 2006 Aug 15;575(Pt 1):101-13. doi: 10.1113/jphysiol.2006.111575. Epub 2006 Jun 1. [PubMed:16740613 ]
Nishiuma T, Nishimura Y, Okada T, Kuramoto E, Kotani Y, Jahangeer S, Nakamura S: Inhalation of sphingosine kinase inhibitor attenuates airway inflammation in asthmatic mouse model. Am J Physiol Lung Cell Mol Physiol. 2008 Jun;294(6):L1085-93. doi: 10.1152/ajplung.00445.2007. Epub 2008 Mar 21. [PubMed:18359884 ]
Jin ZQ, Karliner JS: Low dose N, N-dimethylsphingosine is cardioprotective and activates cytosolic sphingosine kinase by a PKCepsilon dependent mechanism. Cardiovasc Res. 2006 Sep 1;71(4):725-34. doi: 10.1016/j.cardiores.2006.06.010. Epub 2006 Jun 12. [PubMed:16831409 ]
LOTUS database [Link]

Showing NP-Card for n,n-dimethylsphingosine (NP0225469)

MOL for NP0225469 (n,n-dimethylsphingosine)

3D MOL for NP0225469 (n,n-dimethylsphingosine)

3D SDF for NP0225469 (n,n-dimethylsphingosine)

3D-SDF for NP0225469 (n,n-dimethylsphingosine)

PDB for NP0225469 (n,n-dimethylsphingosine)

3D PDB for NP0225469 (n,n-dimethylsphingosine)

SMILES for NP0225469 (n,n-dimethylsphingosine)

INCHI for NP0225469 (n,n-dimethylsphingosine)

Structure for NP0225469 (n,n-dimethylsphingosine)

3D Structure for NP0225469 (n,n-dimethylsphingosine)