MiMeDB: Showing metabocard for Phytosphingosine 1-phosphate (MMDBc0033117)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:35:29 UTC

Update Date

2022-08-31 22:26:22 UTC

Metabolite ID

MMDBc0033117

Metabolite Identification

Common Name

Phytosphingosine 1-phosphate

Description

Phytosphingosine 1-phosphate is an intermediate in sphingolipid metabolism pathway. Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannosyl-diinositol-phosphorylceramide (M(IP)2C). Sphingolipid long chain bases (LCBs) - dihydrosphingosine (DHS) and phytosphingosine (PHS) - are implicated as secondary messengers in vital signaling pathways. [Biocyc SPHINGOLIPID-SYN-PWY]

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222352D          

 26 25  0  0  1  0            999 V2000
   -5.7158    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.1954    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868    0.2171    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -0.1954    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.0204    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    1.0421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.1954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    1.0421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -0.6079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.2171    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    7.8591   -0.1954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3 19  1  6  0  0  0
  3  4  1  0  0  0  0
  4 21  1  1  0  0  0
  4  5  1  0  0  0  0
  5 20  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16  2  1  0  0  0  0
  1 17  1  0  0  0  0
  3 18  1  0  0  0  0
 18 22  1  0  0  0  0
 22 25  1  0  0  0  0
 25 23  2  0  0  0  0
 25 24  1  0  0  0  0
 25 26  1  0  0  0  0
M  END


  Mrv0541 02241222352D          

 26 25  0  0  1  0            999 V2000
   -5.7158    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.1954    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868    0.2171    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -0.1954    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -0.1954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.0204    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    1.0421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.1954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    1.0421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -0.6079    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.2171    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    7.8591   -0.1954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3 19  1  6  0  0  0
  3  4  1  0  0  0  0
  4 21  1  1  0  0  0
  4  5  1  0  0  0  0
  5 20  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16  2  1  0  0  0  0
  1 17  1  0  0  0  0
  3 18  1  0  0  0  0
 18 22  1  0  0  0  0
 22 25  1  0  0  0  0
 25 23  2  0  0  0  0
 25 24  1  0  0  0  0
 25 26  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033117

> <DATABASE_NAME>
MIME

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

> <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)/t16-,17+,18-/m0/s1

> <INCHI_KEY>
AYGOSKULTISFCW-KSZLIROESA-N

> <FORMULA>
C18H40NO6P

> <MOLECULAR_WEIGHT>
397.4871

> <EXACT_MASS>
397.259324529

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
45.651647235812085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
{[(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
3.01

> <JCHEM_LOGP>
2.5619659304474784

> <ALOGPS_LOGS>
-4.37

> <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>
133.24

> <JCHEM_REFRACTIVITY>
103.16379999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.71e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phytosphingosine 1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0     -10.669   0.405   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.336  -0.365   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -0.365   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   0.405   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -0.365   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   0.405   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.365   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.405   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.365   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.405   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.365   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667   0.405   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001  -0.365   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335   0.405   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668  -0.365   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.002   0.405   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -12.003  -0.365   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669   0.405   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       9.336  -1.905   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       6.668  -1.905   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.002   1.945   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      12.003  -0.365   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      13.337   1.945   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      13.337  -1.135   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0      13.337   0.405   0.000  0.00  0.00           P+0
HETATM   26  O   UNK     0      14.670  -0.365   0.000  0.00  0.00           O+0
CONECT    1    2   17                                                       
CONECT    2    1   16                                                       
CONECT    3   19    4   18                                                  
CONECT    4    3   21    5                                                  
CONECT    5    4   20    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    2                                                       
CONECT   17    1                                                            
CONECT   18    3   22                                                       
CONECT   19    3                                                            
CONECT   20    5                                                            
CONECT   21    4                                                            
CONECT   22   18   25                                                       
CONECT   23   25                                                            
CONECT   24   25                                                            
CONECT   25   22   23   24   26                                             
CONECT   26   25                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   50    0
END

Synonyms

Value	Source
Phytosphingosine 1-phosphoric acid	Generator

Molecular Formula

C₁₈H₄₀NO₆P

Average Mass

397.4871

Monoisotopic Mass

397.259324529

IUPAC Name

{[(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl]oxy}phosphonic acid

Traditional Name

phytosphingosine 1-phosphate

CAS Registry Number

Not Available

SMILES

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

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)/t16-,17+,18-/m0/s1

InChI Key

AYGOSKULTISFCW-KSZLIROESA-N

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid 1-phosphate (CHEBI:46970 )
Sphingoid base 1-phosphates (LMSP01050003 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.017 g/L	ALOGPS
logP	3.01	ALOGPS
logP	2.56	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.37	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	133.24 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	103.16 m³·mol⁻¹	ChemAxon
Polarizability	45.65 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-3931000000-49e5f2c92381acd34655	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uea-0139000000-51052f2317a76cb4dc12	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000y-3953000000-99b4d8dc28f886ef18cf	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0005-7940000000-b68e69385ea0b2c2f275	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9238000000-234612104800bd27157d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9210000000-41a7cf446a4c892aa84d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-1972c746e1aeacd464e8	2016-09-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBr0009101	Phytosphingosine	Phytosphingosine 1-phosphate	sphingosine kinase 1		VMH	30371894
MMDBr0009128	Phytosphingosine 1-phosphate	O-Phosphoethanolamine	Not Available		VMH	30371894

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	Human feces; Human saliva	Unknown

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

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

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10883829

PDB ID

Not Available

ChEBI ID

46970

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Phytosphingosine 1-phosphate (MMDBc0033117)

MOL for #<Metabolite:0x00007fdb041bf530>

3D MOL for #<Metabolite:0x00007fdb041bf530>

3D SDF for #<Metabolite:0x00007fdb041bf530>

3D-SDF for #<Metabolite:0x00007fdb041bf530>

PDB for #<Metabolite:0x00007fdb041bf530>

3D PDB for #<Metabolite:0x00007fdb041bf530>

SMILES for #<Metabolite:0x00007fdb041bf530>

INCHI for #<Metabolite:0x00007fdb041bf530>

Structure for #<Metabolite:0x00007fdb041bf530>

3D Structure for #<Metabolite:0x00007fdb041bf530>