MiMeDB: Showing metabocard for Sn-Glycerol-1-phosphate (MMDBc0030212)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:58:35 UTC

Update Date

2022-08-31 17:40:44 UTC

Metabolite ID

MMDBc0030212

Metabolite Identification

Common Name

Sn-Glycerol-1-phosphate

Description

Sn-glycerol-1-phosphate is a glycerol phosphate. It is a key substrate in phospholipid synthesis and phosphatidylglycerol sbiosynthesis. The sn-glycerol-3-phosphate acyltransferase (plsB) of Escherichia coli is a key regulatory enzyme that catalyzes the first committed step in phospholipid biosynthesis. (PMID 9393688 ) Fosmidomycin is a hydrophilic molecule and in many bacteria its uptake is an active process involving a cAMP dependent glycerol-3-phosphate transporter (GlpT). (PMID 18489786 )

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-(Glycerol 3-phosphate)	ChEBI
L-(Glycerol 1-phosphate)	ChEBI
L-Glycerol 1-phosphate	ChEBI
sn-Gro-1-p	ChEBI
D-(Glycerol 3-phosphoric acid)	Generator
L-(Glycerol 1-phosphoric acid)	Generator
L-Glycerol 1-phosphoric acid	Generator
sn-Glycerol-1-phosphoric acid	Generator

Molecular Formula

C₃H₉O₆P

Average Mass

172.0737

Monoisotopic Mass

172.013674532

IUPAC Name

[(2S)-2,3-dihydroxypropoxy]phosphonic acid

Traditional Name

glycerophosphate

CAS Registry Number

5746-57-6

SMILES

[H][C@](O)(CO)COP(O)(O)=O

InChI Identifier

InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m0/s1

InChI Key

AWUCVROLDVIAJX-VKHMYHEASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphates

Direct Parent

Glycerophosphates

Alternative Parents

Substituents

Sn-glycerol-3-phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Secondary alcohol
1,2-diol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

glycerol 1-phosphate (CHEBI:16221 )
sn-glycerol 1-phosphates (CHEBI:16221 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	30.6 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2	ChemAxon
logS	-0.75	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	107.22 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.39 m³·mol⁻¹	ChemAxon
Polarizability	13.45 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-5900000000-64043ee94d742cc4c8a4	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a6r-9400000000-a63f5ba86caa3b7c6ee9	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-cf0fb6dae7ed4a7915cc	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00fr-6900000000-da790cb57078431a7c1a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-cd376066ff1f1f928911	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a6ed4a0320c8229c8621	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014102	NAD	Dihydroxyacetone phosphate	Glycerol-1-phosphate dehydrogenase [NAD(P)+]	Dehydrogenation	RHEA	34755880
MMDBr0014103	NADP(+)	Dihydroxyacetone phosphate	Glycerol-1-phosphate dehydrogenase [NAD(P)+]	Dehydrogenation	RHEA	34755880
MMDBr0014327	(2E,6E,10E)-geranylgeranyl diphosphate	diphosphate	Geranylgeranylglyceryl phosphate synthase	Synthesis	RHEA	34755880
MMDBr0015229	all-trans-heptaprenyl diphosphate	3-heptaprenyl-sn-glycero-1-phosphate	Heptaprenylglyceryl phosphate synthase	Synthesis	RHEA	34755880
MMDBr0016232	Water	Glycerol	D-glycerol 3-phosphate phosphatase	Dephosphorylation; Hydrolysis of bond	RHEA	34755880
MMDBr0016233	Water	Glycerol	D-glycerol 3-phosphate phosphatase	Dephosphorylation	RHEA	34755880
MMDBr0025620	L-Cysteine	Hydrogen Ion	Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase	Transfer of the diacylglyceryl group	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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Archaea/Archaea	Crenarchaeota	20
Bacteria	Firmicutes	55	Human feces; Human ; Catfish ; Cattle
Archaea/Archaea	Euryarchaeota	37
Archaea/Archaea	Thaumarchaeota	2
Archaea/Archaea	Korarchaeota	1
Archaea	Euryarchaeota	2
Archaea	Crenarchaeota	1
Bacteria	Bacteroidetes	4	Human feces
Bacteria	Actinobacteria	1	Human
Eukaryota/Fungi	Ascomycota	2

Exposure Sources

Source Type	Source Sub-type	Species	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

C00623

BioCyc ID

SN-GLYCEROL-1-PHOSPHATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439276

PDB ID

Not Available

ChEBI ID

16221

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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-Glycerol-1-phosphate (MMDBc0030212)

MOL for #<Metabolite:0x00007fd12c8d7d90>

3D MOL for #<Metabolite:0x00007fd12c8d7d90>

3D SDF for #<Metabolite:0x00007fd12c8d7d90>

3D-SDF for #<Metabolite:0x00007fd12c8d7d90>

PDB for #<Metabolite:0x00007fd12c8d7d90>

3D PDB for #<Metabolite:0x00007fd12c8d7d90>

SMILES for #<Metabolite:0x00007fd12c8d7d90>

INCHI for #<Metabolite:0x00007fd12c8d7d90>

Structure for #<Metabolite:0x00007fd12c8d7d90>

3D Structure for #<Metabolite:0x00007fd12c8d7d90>