MiMeDB: Showing metabocard for sn-glycero-3-phosphoethanolamine (MMDBc0032169)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:05:17 UTC

Update Date

2024-04-30 19:54:29 UTC

Metabolite ID

MMDBc0032169

Metabolite Identification

Common Name

sn-glycero-3-phosphoethanolamine

Description

Sn-glycero-3-phosphoethanolamine is a substrate for: Lysoplasmalogenase.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  O   UNK     0    8652.5708652.910   0.000  0.00  0.00           O+0
HETATM    2  P   UNK     0    8653.9028653.680   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0    8655.2378652.910   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8656.5738653.680   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8657.9048652.910   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8659.2408653.680   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0    8653.1358655.011   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8654.6768655.011   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0    8651.2368653.680   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8649.9028652.910   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8648.5688653.680   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8647.2348652.910   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8649.9028651.369   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3    7    8                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    2                                                            
CONECT    8    2                                                            
CONECT    9    1   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

COMPND    HMDB0000114
HETATM    1  N1  UNL     1      -3.966  -0.211   1.056  1.00  0.00           N  
HETATM    2  C1  UNL     1      -3.625  -0.149  -0.344  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.157   0.122  -0.564  1.00  0.00           C  
HETATM    4  O1  UNL     1      -1.806   1.336   0.010  1.00  0.00           O  
HETATM    5  P1  UNL     1      -0.184   1.711  -0.192  1.00  0.00           P  
HETATM    6  O2  UNL     1       0.123   2.853   0.783  1.00  0.00           O  
HETATM    7  O3  UNL     1       0.182   2.269  -1.724  1.00  0.00           O  
HETATM    8  O4  UNL     1       0.829   0.441   0.223  1.00  0.00           O  
HETATM    9  C3  UNL     1       1.642   0.133  -0.862  1.00  0.00           C  
HETATM   10  C4  UNL     1       2.573  -1.023  -0.506  1.00  0.00           C  
HETATM   11  O5  UNL     1       1.798  -2.130  -0.171  1.00  0.00           O  
HETATM   12  C5  UNL     1       3.462  -0.652   0.665  1.00  0.00           C  
HETATM   13  O6  UNL     1       2.682  -0.345   1.774  1.00  0.00           O  
HETATM   14  H1  UNL     1      -3.874  -1.194   1.444  1.00  0.00           H  
HETATM   15  H2  UNL     1      -4.990   0.004   1.134  1.00  0.00           H  
HETATM   16  H3  UNL     1      -4.276   0.588  -0.832  1.00  0.00           H  
HETATM   17  H4  UNL     1      -3.839  -1.140  -0.789  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.934   0.110  -1.648  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.598  -0.716  -0.078  1.00  0.00           H  
HETATM   20  H7  UNL     1      -0.011   1.613  -2.436  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.205   1.011  -1.219  1.00  0.00           H  
HETATM   22  H9  UNL     1       1.041  -0.220  -1.739  1.00  0.00           H  
HETATM   23  H10 UNL     1       3.199  -1.283  -1.380  1.00  0.00           H  
HETATM   24  H11 UNL     1       1.148  -1.886   0.530  1.00  0.00           H  
HETATM   25  H12 UNL     1       4.171   0.145   0.422  1.00  0.00           H  
HETATM   26  H13 UNL     1       4.047  -1.560   0.926  1.00  0.00           H  
HETATM   27  H14 UNL     1       3.158   0.171   2.454  1.00  0.00           H  
CONECT    1    2   14   15
CONECT    2    3   16   17
CONECT    3    4   18   19
CONECT    4    5
CONECT    5    6    6    7    8
CONECT    7   20
CONECT    8    9
CONECT    9   10   21   22
CONECT   10   11   12   23
CONECT   11   24
CONECT   12   13   25   26
CONECT   13   27
END

Synonyms

Value	Source
Glycerophosphorylethanolamine	ChEBI
sn-Glycerol-3-phosphoethanolamine	ChEBI
Glycerophosphoethanolamine	HMDB
GPEA	HMDB
Glycerol 3-phosphoethanolamine	HMDB
Glycerol 3-phosphorylethanolamine	HMDB
Glycerol phosphorylethanolamine	HMDB
Glyceryl-3-phosphorylethanolamine	HMDB
alpha-Glycerophosphorylethanolamine	HMDB
sn-Glycero-3-phosphoethanolamine	HMDB
Α-glycerophosphorylethanolamine	HMDB
Glycerylphosphorylethanolamine	MeSH

Molecular Formula

C₅H₁₄NO₆P

Average Mass

215.1415

Monoisotopic Mass

215.055873697

IUPAC Name

(2-aminoethoxy)(2,3-dihydroxypropoxy)phosphinic acid

Traditional Name

glycerophosphorylethanolamine

CAS Registry Number

Not Available

SMILES

NCCOP(O)(=O)OCC(O)CO

InChI Identifier

InChI=1S/C5H14NO6P/c6-1-2-11-13(9,10)12-4-5(8)3-7/h5,7-8H,1-4,6H2,(H,9,10)

InChI Key

JZNWSCPGTDBMEW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerophosphoethanolamines. These are glycerolipids characterized by an ethanolamine ester of glycerophosphoric acid. As is the case with diacylglycerols, glycerophosphoethanolamines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoethanolamines

Direct Parent

Glycerophosphoethanolamines

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sn-glycerol 3-phosphates (CHEBI:52330 )
phosphoethanolamine (CHEBI:52330 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	36.5 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-3.4	ChemAxon
logS	-0.77	ALOGPS
pKa (Strongest Acidic)	1.87	ChemAxon
pKa (Strongest Basic)	10	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	122.24 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	43.82 m³·mol⁻¹	ChemAxon
Polarizability	19.07 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

Cytoplasm

Biospecimen Locations

Brain
Feces
Liver
Placenta
Prostate

Tissue Locations

Brain
Liver
Placenta
Prostate

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191730	Acyl-protein thioesterase 1	Enzyme	O75608	Homo sapiens
MMDBp0191731	Group XV phospholipase A2	Unknown	Q8NCC3	Homo sapiens
MMDBp0191734	Cytosolic phospholipase A2	Unknown	P47712	Homo sapiens
MMDBp0191740	Acyl-protein thioesterase 2	Enzyme	O95372	Homo sapiens
MMDBp0191744	Eosinophil lysophospholipase	Enzyme	Q05315	Homo sapiens
MMDBp0194171	Glycerophosphodiester phosphodiesterase 1	Unknown	Q9NZC3	Homo sapiens
MMDBp0194172	MHC class I antigen	Enzyme	Q95372	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018538	sn-glycero-3-phosphoethanolamine	Benzyl alcohol	Glycerophosphodiester phosphodiesterase, periplasmic	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	PathBank	31602464
MMDBr0025607	Glycerophosphocholine	sn-glycero-3-phosphoethanolamine	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025608	Glycerophosphocholine	sn-glycero-3-phosphoethanolamine	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025772	oleoyl-CoA	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025773	oleoyl-CoA	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880
MMDBr0025774	sn-glycero-3-phosphoethanolamine	CoA	Glycerophosphocholine acyltransferase 1	Acylation	RHEA	34755880

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	7	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Pig	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	325	Human feces; Human pleural fluid plaque; Human ; Human stool; Human subgingival plaque; Human saliva; Pig ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	139	Human feces; Human sputum; Human ; Human unknown; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Pig	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	12	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	104	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	85	Human feces; Human ; Human appendix biopsy; Human stool; Human saliva; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	21	Human feces; Human pleural fluid plaque; Human ; Human stool; Human subgingival plaque; Human saliva; Pig ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Brain	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0000114

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021895

KNApSAcK ID

Not Available

Chemspider ID

110410

KEGG Compound ID

C01233

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5151

PubChem Compound

123874

PDB ID

Not Available

ChEBI ID

52330

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Nitsch RM, Blusztajn JK, Pittas AG, Slack BE, Growdon JH, Wurtman RJ: Evidence for a membrane defect in Alzheimer disease brain. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1671-5. doi: 10.1073/pnas.89.5.1671. [PubMed:1311847 ]
Kish SJ, Robitaille Y, Ball M, Gilbert J, Deck JH, Chang LJ, Schut L: Glycerophosphoethanolamine concentration is elevated in brain of patients with dominantly inherited olivopontocerebellar atrophy. Neurosci Lett. 1990 Dec 11;120(2):209-11. doi: 10.1016/0304-3940(90)90040-g. [PubMed:2293106 ]
Perry TL, Hansen S, Gandham SS: Postmortem changes of amino compounds in human and rat brain. J Neurochem. 1981 Feb;36(2):406-10. doi: 10.1111/j.1471-4159.1981.tb01608.x. [PubMed:7463068 ]
Nelson C, Moffat B, Jacobsen N, Henzel WJ, Stults JT, King KL, McMurtrey A, Vandlen R, Spencer SA: Glycerophosphorylethanolamine (GPEA) identified as an hepatocyte growth stimulator in liver extracts. Exp Cell Res. 1996 Nov 25;229(1):20-6. doi: 10.1006/excr.1996.0339. [PubMed:8940245 ]
Fallbrook A, Turenne SD, Mamalias N, Kish SJ, Ross BM: Phosphatidylcholine and phosphatidylethanolamine metabolites may regulate brain phospholipid catabolism via inhibition of lysophospholipase activity. Brain Res. 1999 Jul 10;834(1-2):207-10. doi: 10.1016/s0006-8993(99)01570-x. [PubMed:10407117 ]
Jensen JE, Drost DJ, Menon RS, Williamson PC: In vivo brain (31)P-MRS: measuring the phospholipid resonances at 4 Tesla from small voxels. NMR Biomed. 2002 Aug;15(5):338-47. doi: 10.1002/nbm.776. [PubMed:12203225 ]
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for sn-glycero-3-phosphoethanolamine (MMDBc0032169)

MOL for #<Metabolite:0x00007f923895e5a8>

3D MOL for #<Metabolite:0x00007f923895e5a8>

3D SDF for #<Metabolite:0x00007f923895e5a8>

3D-SDF for #<Metabolite:0x00007f923895e5a8>

PDB for #<Metabolite:0x00007f923895e5a8>

3D PDB for #<Metabolite:0x00007f923895e5a8>

SMILES for #<Metabolite:0x00007f923895e5a8>

INCHI for #<Metabolite:0x00007f923895e5a8>

Structure for #<Metabolite:0x00007f923895e5a8>

3D Structure for #<Metabolite:0x00007f923895e5a8>