MiMeDB: Showing metabocard for glycerophosphoserine (MMDBc0032170)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:05:19 UTC

Update Date

2022-08-31 18:31:10 UTC

Metabolite ID

MMDBc0032170

Metabolite Identification

Common Name

glycerophosphoserine

Description

Glycerophosphoserine is a phosphodiester. Glycerophosphoserine is a source of phosphate and glycerol for bacteria. Escherichia coli cytosolic glycerophosphodiester phosphodiesterase, UgpQ has broad substrate specificity toward various glycerophosphodiesters, producing sn-glycerol-3-phosphate and the corresponding alcohols. UgpQ accumulates under conditions of phosphate starvation, suggesting that it allows the utilization of glycerophosphodiesters as a source of phosphate. E. coli K12 possesses two systems the salvage of glycerophosphoryl diesters, the Glp system and the Ugp system. In the Glp system, the glpQ gene encodes a periplasmic glycerophosphoryl diester phosphodiesterase (periplasmic GDP) which hydrolyzes deacylated phospholipids to an alcohol and sn-glycerol-3-phosphate. The latter is then transported into the cell by the GlpT transporter. Periplasmic GDP is specific for the glycerophospho- moiety of the substrate, while the alcohol can be any one of several alcohols. This provides the cell with the capability of channeling a wide variety of glycerophosphodiesters into the glpQT-encoded dissimilatory system. In the Ugp system the diesters are hydrolyzed during transport at the cytoplasmic side of the inner membrane to sn-glycerol-3-phosphate and an alcohol by a cytoplasmic GDP, an enzyme encoded by the ugpQ gene. The Ugp system is induced when the cells are starved for inorganic phospate, which is generates phosphate by the system. In E. coli sn-glycerol-3-phosphate can be further metabolized to dihydroxyacetone phosphate by either of two membrane-bound enzymes, depending on the growth conditions. The presumed role of this process is the salvage of glycerol and glycerol phosphates generated by the breakdown of phospholipids and triacylglycerol.

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533006021516092D          

 16 15  0  0  0  0            999 V2000
   -2.4750    1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.3572    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.1822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.4677    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    0.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.0717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -1.7861    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.4750    0.3572    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.4750    0.3572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3000    1.7861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  5  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  2  0  0  0  0
 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
  2 15  1  0  0  0  0
  1 16  1  0  0  0  0
M  CHG  3   7  -1  13  -1  14   1
M  END
> <DATABASE_ID>
MMDBc0032170

> <DATABASE_NAME>
MIME

> <SMILES>
[NH3+]C(COP([O-])(=O)OCC(O)CO)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14NO8P/c7-5(6(10)11)3-15-16(12,13)14-2-4(9)1-8/h4-5,8-9H,1-3,7H2,(H,10,11)(H,12,13)/p-1

> <INCHI_KEY>
ZWZWYGMENQVNFU-UHFFFAOYSA-M

> <FORMULA>
C6H13NO8P

> <MOLECULAR_WEIGHT>
258.143

> <EXACT_MASS>
258.038426961

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.239195652250675

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-azaniumyl-3-[(2,3-dihydroxypropyl phosphonato)oxy]propanoate

> <ALOGPS_LOGP>
-1.56

> <JCHEM_LOGP>
-4.308619109424487

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.213431235520874

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.508008393069721

> <JCHEM_PKA_STRONGEST_BASIC>
9.37658104597518

> <JCHEM_POLAR_SURFACE_AREA>
166.82

> <JCHEM_REFRACTIVITY>
70.6592

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-ammonio-3-[(2,3-dihydroxypropyl phosphonato)oxy]propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-JUN-15         0                                  
HETATM    1  C   UNK     0      -4.620   3.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.850   2.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.310   2.001   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.540   0.667   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0       0.000   0.667   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0       0.000   2.207   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000  -0.873   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0       1.540   0.667   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.310  -0.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.850  -0.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.620  -2.001   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.160  -2.001   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.850  -3.334   0.000  0.00  0.00           O-1
HETATM   14  N   UNK     0       4.620   0.667   0.000  0.00  0.00           N+1
HETATM   15  O   UNK     0      -4.620   0.667   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -6.160   3.334   0.000  0.00  0.00           O+0
CONECT    1    2   16                                                       
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10                                                            
CONECT   15    2                                                            
CONECT   16    1                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Not Available

Molecular Formula

C₆H₁₃NO₈P

Average Mass

258.143

Monoisotopic Mass

258.038426961

IUPAC Name

2-azaniumyl-3-[(2,3-dihydroxypropyl phosphonato)oxy]propanoate

Traditional Name

2-ammonio-3-[(2,3-dihydroxypropyl phosphonato)oxy]propanoate

CAS Registry Number

Not Available

SMILES

[NH3+]C(COP([O-])(=O)OCC(O)CO)C([O-])=O

InChI Identifier

InChI=1S/C6H14NO8P/c7-5(6(10)11)3-15-16(12,13)14-2-4(9)1-8/h4-5,8-9H,1-3,7H2,(H,10,11)(H,12,13)/p-1

InChI Key

ZWZWYGMENQVNFU-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerophosphoserines. These are lipids containing a glycerol moiety carrying a phosphoserine at the 3-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoserines

Direct Parent

Glycerophosphoserines

Alternative Parents

Substituents

Glycerophosphoserine
Alpha-amino acid
Alpha-amino acid or derivatives
Phosphoethanolamine
Dialkyl phosphate
Alkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
1,2-diol
Amino acid or derivatives
Amino acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Alcohol
Organooxygen compound
Organonitrogen compound
Primary alcohol
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Carbonyl group
Organic oxide
Amine
Organopnictogen compound
Organic oxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	41.1 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-4.3	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	166.82 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	70.66 m³·mol⁻¹	ChemAxon
Polarizability	21.24 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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
MMDBr0018540	glycerophosphoserine	Benzyl alcohol	Glycerophosphodiester phosphodiesterase, periplasmic	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	PathBank	31602464

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
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Other Exposures

Source Type	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

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

75144556

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for glycerophosphoserine (MMDBc0032170)

MOL for #<Metabolite:0x00007f92506c4c08>

3D MOL for #<Metabolite:0x00007f92506c4c08>

3D SDF for #<Metabolite:0x00007f92506c4c08>

3D-SDF for #<Metabolite:0x00007f92506c4c08>

PDB for #<Metabolite:0x00007f92506c4c08>

3D PDB for #<Metabolite:0x00007f92506c4c08>

SMILES for #<Metabolite:0x00007f92506c4c08>

INCHI for #<Metabolite:0x00007f92506c4c08>

Structure for #<Metabolite:0x00007f92506c4c08>

3D Structure for #<Metabolite:0x00007f92506c4c08>