MiMeDB: Showing metabocard for sn-glycero-3-phospho-L-serine (MMDBc0056311)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:31 UTC

Update Date

2025-10-07 16:09:44 UTC

Metabolite ID

MMDBc0056311

Metabolite Identification

Common Name

sn-glycero-3-phospho-L-serine

Description

sn-glycero-3-phospho-L-serine is a phospholipid belonging to the class of glycerophospholipids, characterized by a glycerol backbone, two fatty acid chains, and a phosphate group linked to L-serine. Its chemical structure features a hydrophilic head group that includes the serine amino acid, which imparts anionic properties to the molecule, contributing to its role in membrane dynamics. This metabolite is involved in various biochemical pathways, including the formation of lipid bilayers and membrane structures, as evidenced by studies examining supported lipid bilayers (SLBs) and lipid mixture compositions that incorporate sn-glycero-3-phospho-L-serine. For example, research has shown that DOPS is utilized in lipid mixtures to study membrane morphology and dynamics under varying conditions, including pH changes (PMID:30170491 ). Additionally, it plays a role in the structural features of large unilamellar vesicles (LUVs) and multilamellar vesicles (MLVs) in comparative studies (PMID:36676890 ). The presence of DOPS in complex lipid mixtures has also been highlighted in studies focusing on organelle-specific lipid compositions (PMID:30281310 ), demonstrating its significance in cellular membrane biology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 18 17  0  0  1  0            999 V2000
   -2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  1  0  0  0
  8  1  1  0  0  0  0
  4  9  1  1  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 14  2  1  0  0  0  0
 15  3  1  0  0  0  0
 16 12  1  0  0  0  0
 16 13  2  0  0  0  0
 16 14  1  0  0  0  0
 16 15  1  0  0  0  0
  4 17  1  1  0  0  0
  5 18  1  1  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0056311

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)COP(O)(=O)OC[C@]([H])(N)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/t4-,5+/m1/s1

> <INCHI_KEY>
ZWZWYGMENQVNFU-UHNVWZDZSA-M

> <FORMULA>
C6H13NO8P

> <MOLECULAR_WEIGHT>
258.143

> <EXACT_MASS>
258.038426961

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.98892661791974

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-4.308619109424487

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.2134312355208756

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.508008393069721

> <JCHEM_PKA_STRONGEST_BASIC>
9.37658104597518

> <JCHEM_POLAR_SURFACE_AREA>
162.37

> <JCHEM_REFRACTIVITY>
60.4881

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-3-{[(2R)-2,3-dihydroxypropoxy(hydroxy)phosphoryl]oxy}propanoate

> <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      -4.620   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.850   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.620  -0.000   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      -6.160   2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.620   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       6.160  -2.667   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.850  -4.001   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.000   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.540  -0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   17  H   UNK     0      -3.080   2.667   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       3.080  -2.667   0.000  0.00  0.00           H+0
CONECT    1    4    8                                                       
CONECT    2    4   14                                                       
CONECT    3    5   15                                                       
CONECT    4    1    2    9   17                                             
CONECT    5    3    6    7   18                                             
CONECT    6    5   10   11                                                  
CONECT    7    5                                                            
CONECT    8    1                                                            
CONECT    9    4                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12   16                                                            
CONECT   13   16                                                            
CONECT   14    2   16                                                       
CONECT   15    3   16                                                       
CONECT   16   12   13   14   15                                             
CONECT   17    4                                                            
CONECT   18    5                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

Synonyms

Value	Source
(2S)-2-Ammonio-3-({[(2R)-2,3-dihydroxypropoxy]phosphinato}oxy)propanoate	ChEBI
sn-Glycero-3-phospho-L-serine	ChEBI
sn-Glycero-3-phosphoserine	ChEBI
(2S)-2-Ammonio-3-({[(2R)-2,3-dihydroxypropoxy]phosphinato}oxy)propanoic acid	Generator

Molecular Formula

C₆H₁₃NO₈P

Average Mass

258.143

Monoisotopic Mass

258.038426961

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)COP(O)(=O)OC[C@]([H])(N)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/t4-,5+/m1/s1

InChI Key

ZWZWYGMENQVNFU-UHNVWZDZSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

glycerol 1-phosphoserine(1-) (CHEBI:64765 )
sn-glycerophosphodiester(1-) (CHEBI:64765 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.3	ChemAxon
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	9.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	162.37 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	60.49 m³·mol⁻¹	ChemAxon
Polarizability	20.99 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

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
Eukaryota/Fungi	Ascomycota	1

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

28184671

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57339260

PDB ID

Not Available

ChEBI ID

64765

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 sn-glycero-3-phospho-L-serine (MMDBc0056311)

MOL for #<Metabolite:0x00007faddc2d5780>

3D MOL for #<Metabolite:0x00007faddc2d5780>

3D SDF for #<Metabolite:0x00007faddc2d5780>

3D-SDF for #<Metabolite:0x00007faddc2d5780>

PDB for #<Metabolite:0x00007faddc2d5780>

3D PDB for #<Metabolite:0x00007faddc2d5780>

SMILES for #<Metabolite:0x00007faddc2d5780>

INCHI for #<Metabolite:0x00007faddc2d5780>

Structure for #<Metabolite:0x00007faddc2d5780>

3D Structure for #<Metabolite:0x00007faddc2d5780>