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Showing NP-Card for L-threo-sphinganine (NP0334365)

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Record Information
Version2.0
Created at2024-09-09 23:21:09 UTC
Updated at2024-09-09 23:21:09 UTC
NP-MRD IDNP0334365
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-threo-sphinganine
DescriptionL-threo-sphinganine is also known as L-threo-dihydrosphingosine or L-threo-dhs. L-threo-sphinganine is practically insoluble (in water) and a very weakly acidic compound (based on its pKa). L-threo-sphinganine can be found in a number of food items such as white mustard, narrowleaf cattail, tea, and ucuhuba, which makes L-threo-sphinganine a potential biomarker for the consumption of these food products.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334365 (L-threo-sphinganine)


  Mrv1533007131517152D          

 23 22  0  0  1  0            999 V2000
   -9.3770    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6625    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9480    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2336    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5191    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8046    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0901    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3757    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6612    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9467    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2323    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5178    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8033    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0888    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6256    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7690    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0546    5.4138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3401    5.0013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0546    6.2388    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.4835    5.4138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3401    4.1763    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0546    4.5888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3401    5.8263    0.0000 H   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  4  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  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 17 19  1  1  0  0  0
 20 16  1  0  0  0  0
 18 21  1  1  0  0  0
 17 22  1  1  0  0  0
 18 23  1  1  0  0  0
M  CHG  1  19   1
M  END
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3D MOL for NP0334365 (L-threo-sphinganine)

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3D SDF for NP0334365 (L-threo-sphinganine)

  Mrv1533007131517152D          

 23 22  0  0  1  0            999 V2000
   -9.3770    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6625    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9480    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2336    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5191    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8046    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0901    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3757    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6612    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9467    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2323    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5178    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8033    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0888    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6256    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7690    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0546    5.4138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3401    5.0013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0546    6.2388    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.4835    5.4138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3401    4.1763    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0546    4.5888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3401    5.8263    0.0000 H   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  4  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  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 18 17  1  0  0  0  0
 17 19  1  1  0  0  0
 20 16  1  0  0  0  0
 18 21  1  1  0  0  0
 17 22  1  1  0  0  0
 18 23  1  1  0  0  0
M  CHG  1  19   1
M  END
> <DATABASE_ID>
NP0334365

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]([NH3+])(CO)[C@]([H])(O)CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C18H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17-18,20-21H,2-16,19H2,1H3/p+1/t17-,18-/m1/s1

> <INCHI_KEY>
OTKJDMGTUTTYMP-QZTJIDSGSA-O

> <FORMULA>
C18H40NO2

> <MOLECULAR_WEIGHT>
302.522

> <EXACT_MASS>
302.305355952

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
40.65351388285218

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R)-1,3-dihydroxyoctadecan-2-aminium

> <ALOGPS_LOGP>
2.50

> <JCHEM_LOGP>
4.772594245333334

> <ALOGPS_LOGS>
-6.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.262227395125855

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.419876288941946

> <JCHEM_PKA_STRONGEST_BASIC>
9.287692505029561

> <JCHEM_POLAR_SURFACE_AREA>
68.10000000000001

> <JCHEM_REFRACTIVITY>
102.22219999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.00e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-1,3-dihydroxyoctadecan-2-aminium

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334365 (L-threo-sphinganine)
Download
PDB for NP0334365 (L-threo-sphinganine)
HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0     -17.504  10.106   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -16.170   9.336   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -14.836  10.106   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -13.503   9.336   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -12.169  10.106   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -10.835   9.336   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -9.502  10.106   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.168   9.336   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.834  10.106   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.501   9.336   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.167  10.106   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.833   9.336   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.500  10.106   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.166   9.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.168  10.106   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.169   9.336   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.835  10.106   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.502   9.336   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       3.835  11.646   0.000  0.00  0.00           N+1
HETATM   20  O   UNK     0       6.503  10.106   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.502   7.796   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       3.835   8.566   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.502  10.876   0.000  0.00  0.00           H+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                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   18                                                       
CONECT   16   17   20                                                       
CONECT   17   16   18   19   22                                             
CONECT   18   15   17   21   23                                             
CONECT   19   17                                                            
CONECT   20   16                                                            
CONECT   21   18                                                            
CONECT   22   17                                                            
CONECT   23   18                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   44    0
END

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3D PDB for NP0334365 (L-threo-sphinganine)
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SMILES for NP0334365 (L-threo-sphinganine)
[H][C@@]([NH3+])(CO)[C@]([H])(O)CCCCCCCCCCCCCCC
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INCHI for NP0334365 (L-threo-sphinganine)
InChI=1S/C18H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17-18,20-21H,2-16,19H2,1H3/p+1/t17-,18-/m1/s1
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Synonyms
ValueSource
L-threo-DihydrosphingosineMetaCyc
threo-L-SphinganineMetaCyc
L-threo-DHSMetaCyc
L-threo-Dihydrosphingosine (C18)MetaCyc
L-threo-Sphinganine (C18)MetaCyc
SafingolMetaCyc
Chemical FormulaC18H40NO2
Average Mass302.5220 Da
Monoisotopic Mass302.30536 Da
IUPAC Name(2R,3R)-1,3-dihydroxyoctadecan-2-aminium
Traditional Name(2R,3R)-1,3-dihydroxyoctadecan-2-aminium
CAS Registry NumberNot Available
SMILES
[H][C@@]([NH3+])(CO)[C@]([H])(O)CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C18H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17-18,20-21H,2-16,19H2,1H3/p+1/t17-,18-/m1/s1
InChI KeyOTKJDMGTUTTYMP-QZTJIDSGSA-O
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassOrganic nitrogen compounds  
ClassOrganonitrogen compounds  
Sub ClassAmines  
Direct Parent1,2-aminoalcohols  
Alternative Parents
Substituents
  • Secondary alcohol
    • 

  • 1,2-aminoalcohol
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Alcohol
    • 

  • Organic cation
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.5ALOGPS
logP4.77ChemAxon
logS-6ALOGPS
pKa (Strongest Acidic)14.42ChemAxon
pKa (Strongest Basic)9.29ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area68.1 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity102.22 m³·mol⁻¹ChemAxon
Polarizability40.65 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030974  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound90658247  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available