MiMeDB: Showing metabocard for Glycerophosphoserine (MMDBc0031614)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:41:28 UTC

Update Date

2022-08-31 18:22:30 UTC

Metabolite ID

MMDBc0031614

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

3081457
  Mrv0541 07101213362D          

 30 29  0  0  1  0            999 V2000
    5.6655    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3799    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2530    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0780   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0944    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1293   -0.7631    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5652    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9077    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519    0.6683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7656   -0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4232   -0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1363    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4787    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519    1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3659    1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5087    1.1575    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.1568    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6808    0.1568    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2 12  1  0  0  0  0
  3 14  1  0  0  0  0
  4 11  1  0  0  0  0
  4 27  1  0  0  0  0
  5 28  1  0  0  0  0
  6 15  1  0  0  0  0
  6 29  1  0  0  0  0
  8 16  1  0  0  0  0
  8 30  1  0  0  0  0
  9 16  2  0  0  0  0
 13 10  1  6  0  0  0
 10 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 17  1  0  0  0  0
 12 18  1  0  0  0  0
 12 19  1  0  0  0  0
 13 14  1  0  0  0  0
 13 16  1  0  0  0  0
 13 20  1  0  0  0  0
 14 21  1  0  0  0  0
 14 22  1  0  0  0  0
 15 23  1  0  0  0  0
 15 24  1  0  0  0  0
M  END

3081457
  Mrv0541 07101213362D          

 30 29  0  0  1  0            999 V2000
    5.6655    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3799    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2530    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0780   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0944    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1293   -0.7631    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5652    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9077    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519    0.6683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7656   -0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4232   -0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1363    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4787    0.3918    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519    1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3659    1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -1.4933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5087    1.1575    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.1568    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6808    0.1568    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2 12  1  0  0  0  0
  3 14  1  0  0  0  0
  4 11  1  0  0  0  0
  4 27  1  0  0  0  0
  5 28  1  0  0  0  0
  6 15  1  0  0  0  0
  6 29  1  0  0  0  0
  8 16  1  0  0  0  0
  8 30  1  0  0  0  0
  9 16  2  0  0  0  0
 13 10  1  6  0  0  0
 10 25  1  0  0  0  0
 10 26  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 17  1  0  0  0  0
 12 18  1  0  0  0  0
 12 19  1  0  0  0  0
 13 14  1  0  0  0  0
 13 16  1  0  0  0  0
 13 20  1  0  0  0  0
 14 21  1  0  0  0  0
 14 22  1  0  0  0  0
 15 23  1  0  0  0  0
 15 24  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031614

> <DATABASE_NAME>
MIME

> <SMILES>
[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])OP(=O)(O[H])OC([H])([H])C([H])(O[H])C([H])([H])O[H]

> <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)/t4?,5-/m0/s1

> <INCHI_KEY>
ZWZWYGMENQVNFU-AKGZTFGVSA-N

> <FORMULA>
C6H14NO8P

> <MOLECULAR_WEIGHT>
259.151

> <EXACT_MASS>
259.045702941

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
21.467322628226405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-{[(2,3-dihydroxypropoxy)(hydroxy)phosphoryl]oxy}propanoic acid

> <ALOGPS_LOGP>
-2.80

> <JCHEM_LOGP>
-4.308619109424487

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.213431235520876

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5080083930697228

> <JCHEM_PKA_STRONGEST_BASIC>
9.37658104597518

> <JCHEM_POLAR_SURFACE_AREA>
159.54000000000002

> <JCHEM_REFRACTIVITY>
49.65100000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.96e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-glycerophosphoserine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3081457                                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JUL-12         0                                  
HETATM    1  P   UNK     0      10.576   0.000   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0       9.242  -0.770   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      11.909   0.770   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       6.574  -2.310   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       9.806   1.334   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.907  -0.770   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      11.346  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      17.244   0.770   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      15.910  -1.540   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      14.577   2.310   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       6.574  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.908   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.577   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.243   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.241   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.910   0.000   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0       7.708  -1.425   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       8.522   0.731   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       7.294   0.731   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      15.404   1.247   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      12.629  -0.731   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      13.857  -0.731   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       5.854   0.731   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       4.627   0.731   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      15.404   2.787   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      13.750   2.787   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       5.747  -2.787   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0      10.283   2.161   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       3.080  -0.293   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      18.071   0.293   0.000  0.00  0.00           H+0
CONECT    1    2    3    5    7                                             
CONECT    2    1   12                                                       
CONECT    3    1   14                                                       
CONECT    4   11   27                                                       
CONECT    5    1   28                                                       
CONECT    6   15   29                                                       
CONECT    7    1                                                            
CONECT    8   16   30                                                       
CONECT    9   16                                                            
CONECT   10   13   25   26                                                  
CONECT   11    4   12   15   17                                             
CONECT   12    2   11   18   19                                             
CONECT   13   10   14   16   20                                             
CONECT   14    3   13   21   22                                             
CONECT   15    6   11   23   24                                             
CONECT   16    8    9   13                                                  
CONECT   17   11                                                            
CONECT   18   12                                                            
CONECT   19   12                                                            
CONECT   20   13                                                            
CONECT   21   14                                                            
CONECT   22   14                                                            
CONECT   23   15                                                            
CONECT   24   15                                                            
CONECT   25   10                                                            
CONECT   26   10                                                            
CONECT   27    4                                                            
CONECT   28    5                                                            
CONECT   29    6                                                            
CONECT   30    8                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   58    0
END

Synonyms

Value	Source
1-Glycerophosphoserine	ChEBI
Glycero-1-phosphoserine	ChEBI
L-Serine 1-phosphoglycerol	ChEBI
L-Serine 2,3-dihydroxypropyl hydrogen phosphate	ChEBI
L-Serine 2,3-dihydroxypropyl hydrogen phosphoric acid	Generator
Glycerophosphoserine, 14C-labeled, (R)-isomer	MeSH
Glycerophosphoserine, dipotassium salt, (R)-isomer	MeSH
Glycerophosphoserine, disodium salt, (R)-isomer	MeSH
Glycerophosphoserine, calcium salt (1:1), (R)-isomer	MeSH
Glycerophosphoserine, (R)-isomer	MeSH

Molecular Formula

C₆H₁₄NO₈P

Average Mass

259.151

Monoisotopic Mass

259.045702941

IUPAC Name

(2S)-2-amino-3-{[(2,3-dihydroxypropoxy)(hydroxy)phosphoryl]oxy}propanoic acid

Traditional Name

1-glycerophosphoserine

CAS Registry Number

Not Available

SMILES

[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])OP(=O)(O[H])OC([H])([H])C([H])(O[H])C([H])([H])O[H]

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)/t4?,5-/m0/s1

InChI Key

ZWZWYGMENQVNFU-AKGZTFGVSA-N

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic L-alpha-amino acid (CHEBI:62013 )
L-serine derivative (CHEBI:62013 )
glycerol 1-phosphodiester (CHEBI:62013 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.6 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-4.3	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	159.54 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	49.65 m³·mol⁻¹	ChemAxon
Polarizability	21.47 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	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

CPD0-2030

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3081457

PDB ID

Not Available

ChEBI ID

62013

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for Glycerophosphoserine (MMDBc0031614)

MOL for #<Metabolite:0x00007f124111faf8>

3D MOL for #<Metabolite:0x00007f124111faf8>

3D SDF for #<Metabolite:0x00007f124111faf8>

3D-SDF for #<Metabolite:0x00007f124111faf8>

PDB for #<Metabolite:0x00007f124111faf8>

3D PDB for #<Metabolite:0x00007f124111faf8>

SMILES for #<Metabolite:0x00007f124111faf8>

INCHI for #<Metabolite:0x00007f124111faf8>

Structure for #<Metabolite:0x00007f124111faf8>

3D Structure for #<Metabolite:0x00007f124111faf8>