MiMeDB: Showing metabocard for S-Methyl 3-phospho-1-thio-D-glycerate (MMDBc0033128)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:35:53 UTC

Update Date

2025-10-07 16:07:55 UTC

Metabolite ID

MMDBc0033128

Metabolite Identification

Common Name

S-Methyl 3-phospho-1-thio-D-glycerate

Description

S-Methyl 3-phospho-1-thio-D-glycerate is a thioester compound belonging to the class of phosphonates. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      18.693 -12.242   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.366 -13.022   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.038 -12.242   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      17.366 -14.558   0.000  0.00  0.00           O+0
HETATM    5  S   UNK     0      14.704 -13.022   0.000  0.00  0.00           S+0
HETATM    6  O   UNK     0      16.038 -10.706   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      13.395 -12.273   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      20.027 -13.022   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      22.695 -13.022   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      21.361 -10.712   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      21.361 -12.252   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      21.760 -13.740   0.000  0.00  0.00           O+0
CONECT    1    8    2                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5    6                                                  
CONECT    4    2                                                            
CONECT    5    3    7                                                       
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8    1   11                                                       
CONECT    9   11                                                            
CONECT   10   11                                                            
CONECT   11    8    9   10   12                                             
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
S-Methyl-3-phospho-1-thio-D-glycerate	ChEBI
S-Methyl-3-phospho-1-thio-D-glyceric acid	Generator
S-Methyl 3-phospho-1-thio-D-glyceric acid	Generator

Molecular Formula

C₄H₉O₆PS

Average Mass

216.149

Monoisotopic Mass

215.985745222

IUPAC Name

[(2R)-2-hydroxy-3-(methylsulfanyl)-3-oxopropoxy]phosphonic acid

Traditional Name

(2R)-2-hydroxy-3-(methylsulfanyl)-3-oxopropoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H9O6PS/c1-12-4(6)3(5)2-10-11(7,8)9/h3,5H,2H2,1H3,(H2,7,8,9)/t3-/m1/s1

InChI Key

VSSDMJHMYISZJU-GSVOUGTGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Monosaccharide
Secondary alcohol
Thiocarboxylic acid ester
Carbothioic s-ester
Sulfenyl compound
Thiocarboxylic acid or derivatives
Carboxylic acid derivative
Alcohol
Organosulfur compound
Organooxygen compound
Organic oxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

thioester (CHEBI:15880 )
aldonate ester phosphate (CHEBI:15880 )
carbohydrate acid ester (CHEBI:15880 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	24.6 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-0.74	ChemAxon
logS	-0.94	ALOGPS
pKa (Strongest Acidic)	1.36	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	42.32 m³·mol⁻¹	ChemAxon
Polarizability	17.76 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 (Non-derivatized) - 70eV, Positive	splash10-0002-9300000000-3f90cea089976ac544de	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-1980000000-506ba55d920bfc77c2e7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-3910000000-fecc5e55e39eec080773	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-5900000000-6fe54acd135425c48e8f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-9220000000-cededc1c17e9c0782193	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-13f50f7f6e27d9f0fc83	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-1b7e80786893cf7aa351	2016-09-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	496.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	398.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	40.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	255.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	287.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	308.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	481.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	766.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	737.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	178.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	365.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	188.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	42.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	392.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	713.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	51.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	245.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	614.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	607.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_1	CSC(=O)[C@@H](COP(=O)(O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1985.86
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_2	CSC(=O)[C@H](O)COP(=O)(O)O[Si](C)(C)C	standard non polar	2025-10-24	2113.42
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_3	CSC(=O)[C@@H](COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1835.22
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_4	CSC(=O)[C@H](O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1937.83
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_5	CSC(=O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2164.66
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_1	CSC(=O)[C@@H](COP(=O)(O)O)O[Si](C)(C)C	standard polar	2025-10-24	2347.77
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_2	CSC(=O)[C@H](O)COP(=O)(O)O[Si](C)(C)C	standard polar	2025-10-24	2226.74
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_3	CSC(=O)[C@@H](COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2378.94
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_4	CSC(=O)[C@H](O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1856.56
Gas Chromatography	S-Methyl 3-phospho-1-thio-D-glycerate_TMS_5	CSC(=O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1824.59

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	Human feces; Human saliva	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

C04399

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440324

PDB ID

Not Available

ChEBI ID

15880

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

BLACK S, WRIGHT NG: Enzymatic formation of glyceryl and phosphoglyceryl methylthiol esters. J Biol Chem. 1956 Jul;221(1):171-80. [PubMed:13345808 ]
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D: BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6. doi: 10.1093/nar/gkq1089. Epub 2010 Nov 9. [PubMed:21062828 ]

Showing metabocard for S-Methyl 3-phospho-1-thio-D-glycerate (MMDBc0033128)

MOL for #<Metabolite:0x00007f8adbd6fed0>

3D MOL for #<Metabolite:0x00007f8adbd6fed0>

3D SDF for #<Metabolite:0x00007f8adbd6fed0>

3D-SDF for #<Metabolite:0x00007f8adbd6fed0>

PDB for #<Metabolite:0x00007f8adbd6fed0>

3D PDB for #<Metabolite:0x00007f8adbd6fed0>

SMILES for #<Metabolite:0x00007f8adbd6fed0>

INCHI for #<Metabolite:0x00007f8adbd6fed0>

Structure for #<Metabolite:0x00007f8adbd6fed0>

3D Structure for #<Metabolite:0x00007f8adbd6fed0>