MiMeDB: Showing metabocard for (4R)-hydroxysphinganine (MMDBc0054955)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:38:33 UTC

Update Date

2022-08-12 20:09:10 UTC

Metabolite ID

MMDBc0054955

Metabolite Identification

Common Name

(4R)-hydroxysphinganine

Description

phytosphingosine(1+), also known as (4R)-hydroxysphinganine, belongs to the class of organic compounds known as 1,3-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 C3 atom. Based on a literature review a significant number of articles have been published on phytosphingosine(1+).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221382D          

 25 24  0  0  1  0            999 V2000
    7.9480    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
    9.3770    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0914    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8059    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5204    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2349    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9493    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6638    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3783    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0927    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8072    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5217    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2362    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0940    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3796    5.4138    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.9506    5.4138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6651    5.0013    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.3796    6.2388    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   20.8085    5.4138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9506    6.2388    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6651    4.1763    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3796    4.5888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.9506    4.5888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.6651    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
 16 15  1  0  0  0  0
 17 14  1  0  0  0  0
 18 16  1  0  0  0  0
 18 17  1  0  0  0  0
 16 19  1  6  0  0  0
 20 15  1  0  0  0  0
 17 21  1  6  0  0  0
 18 22  1  1  0  0  0
 16 23  1  6  0  0  0
 17 24  1  6  0  0  0
 18 25  1  1  0  0  0
M  CHG  1  19   1
M  END
> <DATABASE_ID>
MMDBc0054955

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H39NO3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(21)18(22)16(19)15-20/h16-18,20-22H,2-15,19H2,1H3/p+1/t16-,17+,18-/m0/s1

> <INCHI_KEY>
AERBNCYCJBRYDG-KSZLIROESA-O

> <FORMULA>
C18H40NO3

> <MOLECULAR_WEIGHT>
318.521

> <EXACT_MASS>
318.300270572

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
41.495354781245354

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-aminium

> <JCHEM_LOGP>
3.6976906383333326

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.815152200058375

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.447718983386185

> <JCHEM_PKA_STRONGEST_BASIC>
8.908333300303687

> <JCHEM_POLAR_SURFACE_AREA>
88.33000000000001

> <JCHEM_REFRACTIVITY>
103.58369999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxysphinganine(1+)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      14.836  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      17.504  10.106   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.837   9.336   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.171  10.106   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.505   9.336   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.838  10.106   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      24.172   9.336   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.506  10.106   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.839   9.336   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.173  10.106   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      29.507   9.336   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      30.840  10.106   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      32.174   9.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      37.509   9.336   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      36.175  10.106   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      33.508  10.106   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      34.842   9.336   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      36.175  11.646   0.000  0.00  0.00           N+1
HETATM   20  O   UNK     0      38.843  10.106   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      33.508  11.646   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      34.842   7.796   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0      36.175   8.566   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      33.508   8.566   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      34.842  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   17                                                       
CONECT   15   16   20                                                       
CONECT   16   15   18   19   23                                             
CONECT   17   14   18   21   24                                             
CONECT   18   16   17   22   25                                             
CONECT   19   16                                                            
CONECT   20   15                                                            
CONECT   21   17                                                            
CONECT   22   18                                                            
CONECT   23   16                                                            
CONECT   24   17                                                            
CONECT   25   18                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   48    0
END

Synonyms

Value	Source
(4R)-Hydroxysphinganine	ChEBI
4-Hydroxysphinganine(1+)	ChEBI
4-Hydroxysphinganinium(1+)	ChEBI
Phytosphingosinium(1+)	ChEBI

Molecular Formula

C₁₈H₄₀NO₃

Average Mass

318.521

Monoisotopic Mass

318.300270572

IUPAC Name

(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-aminium

Traditional Name

4-hydroxysphinganine(1+)

CAS Registry Number

Not Available

SMILES

[H][C@]([NH3+])(CO)[C@]([H])(O)[C@]([H])(O)CCCCCCCCCCCCCC

InChI Identifier

InChI=1S/C18H39NO3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(21)18(22)16(19)15-20/h16-18,20-22H,2-15,19H2,1H3/p+1/t16-,17+,18-/m0/s1

InChI Key

AERBNCYCJBRYDG-KSZLIROESA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,3-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 C3 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,3-aminoalcohols

Alternative Parents

Substituents

1,3-aminoalcohol
Secondary alcohol
1,2-aminoalcohol
Polyol
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Primary aliphatic amine
Alcohol
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid base(1+) (CHEBI:64124 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	3.7	ChemAxon
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	8.91	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	88.33 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	103.58 m³·mol⁻¹	ChemAxon
Polarizability	41.5 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

PHYTOSPINGOSINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56927898

PDB ID

Not Available

ChEBI ID

64124

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (4R)-hydroxysphinganine (MMDBc0054955)

MOL for #<Metabolite:0x00007fdb3c2a9738>

3D MOL for #<Metabolite:0x00007fdb3c2a9738>

3D SDF for #<Metabolite:0x00007fdb3c2a9738>

3D-SDF for #<Metabolite:0x00007fdb3c2a9738>

PDB for #<Metabolite:0x00007fdb3c2a9738>

3D PDB for #<Metabolite:0x00007fdb3c2a9738>

SMILES for #<Metabolite:0x00007fdb3c2a9738>

INCHI for #<Metabolite:0x00007fdb3c2a9738>

Structure for #<Metabolite:0x00007fdb3c2a9738>

3D Structure for #<Metabolite:0x00007fdb3c2a9738>