MiMeDB: Showing metabocard for (4R)-hydroxysphinganine 1-phosphate (MMDBc0054956)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:38:34 UTC

Update Date

2024-04-20 06:15:01 UTC

Metabolite ID

MMDBc0054956

Metabolite Identification

Common Name

(4R)-hydroxysphinganine 1-phosphate

Description

phytosphingosine 1-phosphate(1-), also known as (4R)-hydroxysphinganine 1-phosphate, 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. Based on a literature review a significant number of articles have been published on phytosphingosine 1-phosphate(1-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221382D          

 29 28  0  0  1  0            999 V2000
    6.8211   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5355   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2500   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9645   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6789   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3934   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1079   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8224   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5368   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2513   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9658   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6802   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3947   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1092   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9671   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2526   -4.2868    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.8237   -4.2868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.5381   -3.8743    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2526   -5.1118    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8237   -5.1118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5381   -3.0493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.1105   -3.4618    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   20.8085   -4.5888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.9835   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6815   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.3960   -3.8743    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   18.2526   -3.4618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.8237   -3.4618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5381   -4.6993    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  1  0  0  0
 17 20  1  1  0  0  0
 18 21  1  6  0  0  0
 25 15  1  0  0  0  0
 26 22  1  0  0  0  0
 26 23  1  0  0  0  0
 26 24  2  0  0  0  0
 26 25  1  0  0  0  0
 16 27  1  1  0  0  0
 17 28  1  1  0  0  0
 18 29  1  6  0  0  0
M  CHG  1  22  -1
M  END


  Mrv1652306172221382D          

 29 28  0  0  1  0            999 V2000
    6.8211   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5355   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2500   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9645   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6789   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3934   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1079   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8224   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5368   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2513   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9658   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6802   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3947   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1092   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9671   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2526   -4.2868    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.8237   -4.2868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.5381   -3.8743    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.2526   -5.1118    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8237   -5.1118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5381   -3.0493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.1105   -3.4618    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   20.8085   -4.5888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.9835   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6815   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.3960   -3.8743    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   18.2526   -3.4618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.8237   -3.4618    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5381   -4.6993    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  1  0  0  0
 17 20  1  1  0  0  0
 18 21  1  6  0  0  0
 25 15  1  0  0  0  0
 26 22  1  0  0  0  0
 26 23  1  0  0  0  0
 26 24  2  0  0  0  0
 26 25  1  0  0  0  0
 16 27  1  1  0  0  0
 17 28  1  1  0  0  0
 18 29  1  6  0  0  0
M  CHG  1  22  -1
M  END
> <DATABASE_ID>
MMDBc0054956

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(COP(O)([O-])=O)[C@]([H])(O)[C@]([H])(O)CCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C18H40NO6P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(20)18(21)16(19)15-25-26(22,23)24/h16-18,20-21H,2-15,19H2,1H3,(H2,22,23,24)/p-1/t16-,17+,18-/m0/s1

> <INCHI_KEY>
AYGOSKULTISFCW-KSZLIROESA-M

> <FORMULA>
C18H39NO6P

> <MOLECULAR_WEIGHT>
396.485

> <EXACT_MASS>
396.252048558

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
45.712684116510026

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S,4R)-2-amino-1-(hydrogen phosphonooxy)octadecane-3,4-diol

> <JCHEM_LOGP>
2.5619659304474784

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.540655024704243

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5142211495907771

> <JCHEM_PKA_STRONGEST_BASIC>
9.371028873380947

> <JCHEM_POLAR_SURFACE_AREA>
136.07

> <JCHEM_REFRACTIVITY>
102.04209999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R)-2-amino-1-(hydrogen phosphonooxy)octadecane-3,4-diol

> <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      12.733  -8.002   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.066  -7.232   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.400  -8.002   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.734  -7.232   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.067  -8.002   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.401  -7.232   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.735  -8.002   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.068  -7.232   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.402  -8.002   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      24.736  -7.232   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.069  -8.002   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      27.403  -7.232   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      28.737  -8.002   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.070  -7.232   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      35.405  -7.232   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      34.072  -8.002   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      31.404  -8.002   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      32.738  -7.232   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      34.072  -9.542   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0      31.404  -9.542   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      32.738  -5.692   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      39.406  -6.462   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0      38.843  -8.566   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      37.303  -5.898   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      36.739  -8.002   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      38.073  -7.232   0.000  0.00  0.00           P+0
HETATM   27  H   UNK     0      34.072  -6.462   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0      31.404  -6.462   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0      32.738  -8.772   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   25                                                       
CONECT   16   15   18   19   27                                             
CONECT   17   14   18   20   28                                             
CONECT   18   16   17   21   29                                             
CONECT   19   16                                                            
CONECT   20   17                                                            
CONECT   21   18                                                            
CONECT   22   26                                                            
CONECT   23   26                                                            
CONECT   24   26                                                            
CONECT   25   15   26                                                       
CONECT   26   22   23   24   25                                             
CONECT   27   16                                                            
CONECT   28   17                                                            
CONECT   29   18                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   56    0
END

Synonyms

Value	Source
(2S,3S,4R)-2-Ammonio-3,4-dihydroxyoctadecyl phosphate	ChEBI
(4R)-Hydroxysphinganine 1-phosphate	ChEBI
(2S,3S,4R)-2-Ammonio-3,4-dihydroxyoctadecyl phosphoric acid	Generator
(4R)-Hydroxysphinganine 1-phosphoric acid	Generator
Phytosphingosine 1-phosphoric acid(1-)	Generator

Molecular Formula

C₁₈H₃₉NO₆P

Average Mass

396.485

Monoisotopic Mass

396.252048558

IUPAC Name

(2S,3S,4R)-2-amino-1-(hydrogen phosphonooxy)octadecane-3,4-diol

Traditional Name

(2S,3S,4R)-2-amino-1-(hydrogen phosphonooxy)octadecane-3,4-diol

CAS Registry Number

Not Available

SMILES

[H][C@](N)(COP(O)([O-])=O)[C@]([H])(O)[C@]([H])(O)CCCCCCCCCCCCCC

InChI Identifier

InChI=1S/C18H40NO6P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(20)18(21)16(19)15-25-26(22,23)24/h16-18,20-21H,2-15,19H2,1H3,(H2,22,23,24)/p-1/t16-,17+,18-/m0/s1

InChI Key

AYGOSKULTISFCW-KSZLIROESA-M

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
Phosphoethanolamine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
1,3-aminoalcohol
1,2-aminoalcohol
1,2-diol
Secondary alcohol
Organic nitrogen compound
Organic oxygen compound
Primary amine
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Amine
Alcohol
Organopnictogen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid 1-phosphate(1-) (CHEBI:64795 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	2.56	ChemAxon
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.37	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	136.07 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	102.04 m³·mol⁻¹	ChemAxon
Polarizability	45.71 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

Source Type	Source Sub-type	Species	Data Source	Reference

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

28184683

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24113330

PDB ID

Not Available

ChEBI ID

64795

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 1-phosphate (MMDBc0054956)

MOL for #<Metabolite:0x00007feca6bc8028>

3D MOL for #<Metabolite:0x00007feca6bc8028>

3D SDF for #<Metabolite:0x00007feca6bc8028>

3D-SDF for #<Metabolite:0x00007feca6bc8028>

PDB for #<Metabolite:0x00007feca6bc8028>

3D PDB for #<Metabolite:0x00007feca6bc8028>

SMILES for #<Metabolite:0x00007feca6bc8028>

INCHI for #<Metabolite:0x00007feca6bc8028>

Structure for #<Metabolite:0x00007feca6bc8028>

3D Structure for #<Metabolite:0x00007feca6bc8028>