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sn-Glycerol 3-phosphate

PubChem CID
439162
Structure
sn-Glycerol 3-phosphate_small.png
sn-Glycerol 3-phosphate_3D_Structure.png
Molecular Formula
Synonyms
  • sn-Glycerol 3-phosphate
  • 17989-41-2
  • D-Glycerol 1-phosphate
  • (R)-glycerol 1-phosphate
  • sn-Glycero-3-phosphate
Molecular Weight
172.07 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-04
Description
Sn-glycerol 3-phosphate is an sn-glycerol 3-phosphate having unsubstituted hydroxy groups. It has a role as a human metabolite, a plant metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a glycerol 1-phosphate and a member of sn-glycerol 3-phosphates. It is functionally related to a glycerol. It is a conjugate acid of a sn-glycerol 3-phosphate(2-). It is an enantiomer of a sn-glycerol 1-phosphate.
glycerol-3-phosphate is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).
sn-Glycerol 3-phosphate has been reported in Glycine max, Vicia faba, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
sn-Glycerol 3-phosphate.png

1.2 3D Conformer

2 Biologic Description

IUPAC Condensed
PA(0:0/0:0)
IUPAC
sn-glycerol-3-phosphate

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

[(2R)-2,3-dihydroxypropyl] dihydrogen phosphate
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m1/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

AWUCVROLDVIAJX-GSVOUGTGSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C([C@H](COP(=O)(O)O)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C3H9O6P
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

57-03-4

3.3.2 UNII

3.3.3 ChEBI ID

3.3.4 ChEMBL ID

3.3.5 DrugBank ID

3.3.6 DSSTox Substance ID

3.3.7 HMDB ID

3.3.8 KEGG ID

3.3.9 Nikkaji Number

3.3.10 Wikidata

3.4 Synonyms

3.4.1 MeSH Entry Terms

MeSH Entry Terms for alpha-glycerophosphoric acid
  • 1-phosphoglycerol
  • alpha-glycerophosphate
  • alpha-glycerophosphoric acid
  • alpha-glycerophosphoric acid, (DL)-isomer
  • alpha-glycerophosphoric acid, (R)-isomer
  • alpha-glycerophosphoric acid, (S)-isomer
  • alpha-glycerophosphoric acid, 1,2,3-propanetriol-1-(18)O,3-(dihydrogen phosphate)-labeled
  • alpha-glycerophosphoric acid, 1,2,3-propanetriol-2-(18)O,3-(dihydrogen phosphate)-labeled
  • alpha-glycerophosphoric acid, calcium salt
  • alpha-glycerophosphoric acid, disodium salt
  • alpha-glycerophosphoric acid, disodium salt (+-)-isomer
  • alpha-glycerophosphoric acid, disodium salt hexahydrate(+-)-isomer
  • alpha-glycerophosphoric acid, Fe salt
  • alpha-glycerophosphoric acid, Fe(+3) salt (3:2)
  • alpha-glycerophosphoric acid, monocalcium salt
  • alpha-glycerophosphoric acid, monocalcium salt (S)-isomer
  • alpha-glycerophosphoric acid, monomagnesium salt
  • alpha-glycerophosphoric acid, sodium salt
  • disodium glycerophosphate
  • glycerol 1-phosphate
  • glycerol 3-phosphate
  • sodium glycerophosphate
MeSH Entry Terms for Glycerophosphates
  • Calcium Glycerophosphate
  • Glycerolphosphate
  • Glycerolphosphates
  • Glycerophosphate
  • Glycerophosphate, Calcium
  • Glycerophosphates

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
172.07 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-2.9
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
172.01367500 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
172.01367500 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
107 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
10
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
129
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
1
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

4.2 Experimental Properties

4.2.1 Physical Description

Solid

4.2.2 Melting Point

102 - 104 °C

4.2.3 Solubility

1000.0 mg/mL

4.2.4 Collision Cross Section

132 Ų [M+Na]+ [CCS Type: TW; Method: calibrated with polyalanine]

142.16 Ų [M+Na]+ [CCS Type: DT; Method: stepped-field]

179.49 Ų [M+H]+ [CCS Type: DT; Method: stepped-field]

130.8 Ų [M-H]- [CCS Type: DT; Method: stepped-field]

137.2 Ų [M+Na]+

127.4 Ų [M-H]-

S50 | CCSCOMPEND | The Unified Collision Cross Section (CCS) Compendium | DOI:10.5281/zenodo.2658162

4.3 Chemical Classes

4.3.1 Drugs

Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

5 Spectral Information

5.1 1D NMR Spectra

5.1.1 1H NMR Spectra

Spectra ID
Instrument Type
Varian
Frequency
600 MHz
Solvent
Water
pH
7.00
Shifts [ppm]:Intensity
3.83:75.87, 3.79:64.70, 3.85:24.21, 3.76:7.27, 3.87:33.23, 3.86:64.61, 3.68:54.30, 3.76:23.85, 3.83:33.44, 3.59:50.32, 3.62:84.50, 3.67:100.00, 3.84:27.03, 3.82:48.99, 3.86:32.20, 3.84:20.68, 3.81:44.84, 3.66:89.10, 3.86:43.39, 3.61:76.87, 3.77:31.48, 3.77:30.16, 3.78:42.09, 3.84:41.22, 3.80:47.24, 3.84:14.31, 3.60:56.87, 3.69:56.75, 3.85:42.09, 3.87:12.26, 3.85:56.84, 3.78:52.55, 3.81:60.24, 3.79:70.65
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5.2 2D NMR Spectra

5.2.1 1H-1H NMR Spectra

2D NMR Spectra Type
1H-1H TOCSY
Spectra ID
Shifts [ppm] (F2:F1)
3.68:3.67, 3.68:3.68, 3.62:3.85, 3.96:3.78, 3.62:3.81, 3.67:3.62, 3.67:3.84, 3.61:3.61, 3.81:3.79, 4.15:4.14, 3.67:3.79, 3.66:3.58, 3.68:4.15, 3.83:3.67, 3.62:3.66, 3.62:3.70, 3.85:3.85, 3.96:3.85, 3.62:3.83, 3.83:3.62, 3.67:3.83, 3.81:3.69, 3.81:3.81, 3.70:3.57, 4.15:3.68, 4.16:4.16, 3.81:3.78, 3.67:3.81
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5.2.2 1H-13C NMR Spectra

2D NMR Spectra Type
1H-13C HSQC
Spectra ID
Instrument Type
Bruker
Frequency
600 MHz
Solvent
Water
pH
7.00
Shifts [ppm] (F2:F1):Intensity
3.68:65.00:0.65, 3.82:67.58:0.76, 3.86:74.05:1.00, 3.61:65.00:0.82, 3.78:67.58:0.74
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5.3 Mass Spectrometry

5.3.1 GC-MS

1 of 4
View All
Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

101.0 100

133.0 84.98

299.0 72.57

147.0 68.97

103.0 68.27

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Notes
instrument=Leco Pegasus IV
2 of 4
View All
MS Category
Experimental
MS Type
GC-MS
MS Level
MS1
Instrument
Leco Pegasus IV
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

101 100

133 84.98

299 72.57

147 68.97

103 68.27

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5.3.2 MS-MS

1 of 6
View All
Spectra ID
Instrument Type
Quattro_QQQ
Ionization Mode
Positive
Top 5 Peaks

99.0 100

173.0 24.31

98.0 7.38

75.0 7.09

57.0 3.40

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Notes
delivery=Flow_Injectionanalyzer=Triple_Quad
2 of 6
View All
Spectra ID
Instrument Type
Quattro_QQQ
Ionization Mode
Positive
Top 5 Peaks

81.0 100

99.0 74.97

98.0 13.87

57.0 12.30

173.0 9.85

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Notes
delivery=Flow_Injectionanalyzer=Triple_Quad

5.3.3 LC-MS

1 of 10
View All
Authors
Kakazu Y, Horai H, Institute for Advanced Biosciences, Keio Univ.
Instrument
API3000, Applied Biosystems
Instrument Type
LC-ESI-QQ
MS Level
MS2
Ionization Mode
POSITIVE
Collision Energy
10 V
Precursor m/z
173
Precursor Adduct
[M+H]+
Top 5 Peaks

156.2 999

173.3 881

104.9 785

141.3 403

80.7 313

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License
CC BY-NC-SA
2 of 10
View All
Authors
Kakazu Y, Horai H, Institute for Advanced Biosciences, Keio Univ.
Instrument
API3000, Applied Biosystems
Instrument Type
LC-ESI-QQ
MS Level
MS2
Ionization Mode
POSITIVE
Collision Energy
20 V
Precursor m/z
173
Precursor Adduct
[M+H]+
Top 5 Peaks

109.2 999

80.9 981

105.1 727

141.4 545

138 490

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License
CC BY-NC-SA

5.3.4 Other MS

1 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
173.13
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
positive
Collision Energy
30
Top 5 Peaks

99 100

98 38.27

57 14.95

81 7.44

97 4.24

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2 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
171.1
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
negative
Collision Energy
10
Top 5 Peaks

171 100

79 7.48

170 5.69

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7 Chemical Vendors

8 Drug and Medication Information

8.1 Biomarker Information

9 Food Additives and Ingredients

9.1 Associated Foods

10 Pharmacology and Biochemistry

10.1 Human Metabolite Information

10.1.1 Tissue Locations

  • Placenta
  • Prostate

10.1.2 Cellular Locations

  • Cytoplasm
  • Mitochondria

10.1.3 Metabolite Pathways

10.2 Biochemical Reactions

11 Associated Disorders and Diseases

Disease
Colorectal cancer
References

PubMed: 7482520, 19006102, 23940645, 24424155, 20156336, 19678709, 22148915, 25105552, 21773981, 25037050, 27015276, 27107423, 27275383, 28587349

Silke Matysik, Caroline Ivanne Le Roy, Gerhard Liebisch, Sandrine Paule Claus. Metabolomics of fecal samples: A practical consideration. Trends in Food Science & Technology. Vol. 57, Part B, Nov. 2016, p.244-255: http://www.sciencedirect.com/science/article/pii/S0924224416301984

Disease
Frontotemporal dementia
References
PubMed: 23857558
Disease
Lewy body disease
References
PubMed: 23857558

12 Literature

12.1 Consolidated References

12.2 NLM Curated PubMed Citations

12.3 Springer Nature References

12.4 Chemical Co-Occurrences in Literature

12.5 Chemical-Gene Co-Occurrences in Literature

12.6 Chemical-Disease Co-Occurrences in Literature

13 Patents

13.1 Depositor-Supplied Patent Identifiers

13.2 WIPO PATENTSCOPE

13.3 Chemical Co-Occurrences in Patents

13.4 Chemical-Disease Co-Occurrences in Patents

13.5 Chemical-Gene Co-Occurrences in Patents

14 Interactions and Pathways

14.1 Protein Bound 3D Structures

14.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

14.2 Chemical-Target Interactions

14.3 Pathways

15 Biological Test Results

15.1 BioAssay Results

16 Taxonomy

WormJam Metabolites Local CSV for MetFrag | DOI:10.5281/zenodo.3403364
WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series, Worm, 6:2, e1373939, DOI:10.1080/21624054.2017.1373939
Zebrafish Pathway Metabolite MetFrag Local CSV (Beta) | DOI:10.5281/zenodo.3457553
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

17 Classification

17.1 MeSH Tree

17.2 ChEBI Ontology

17.3 KEGG: Risk Category of Japanese OTC Drugs

17.4 ChemIDplus

17.5 NORMAN Suspect List Exchange Classification

17.6 CCSBase Classification

17.7 EPA DSSTox Classification

17.8 LOTUS Tree

17.9 Glycan Naming and Subsumption Ontology (GNOme)

17.10 MolGenie Organic Chemistry Ontology

18 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  4. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  6. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  7. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  8. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Sn-Gro-1-P
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  9. ChEBI
  10. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  11. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  12. Yeast Metabolome Database (YMDB)
    LICENSE
    YMDB is offered to the public as a freely available resource.
    http://www.ymdb.ca/downloads
  13. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  14. ECI Group, LCSB, University of Luxembourg
    LICENSE
    Data: CC-BY 4.0; Code: Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    sn-glycerol 3-phosphate
  15. Natural Product Activity and Species Source (NPASS)
    [(2R)-2,3-Dihydroxypropyl] Dihydrogen Phosphate
    https://bidd.group/NPASS/compound.php?compoundID=NPC266566
  16. FooDB
    LICENSE
    FooDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (FooDB) and the original publication.
    https://foodb.ca/about
  17. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  18. Japan Chemical Substance Dictionary (Nikkaji)
  19. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
    Risk category of Japanese OTC drugs
    http://www.genome.jp/kegg-bin/get_htext?br08312.keg
  20. MarkerDB
    LICENSE
    This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
    https://markerdb.ca/
  21. MassBank Europe
  22. Protein Data Bank in Europe (PDBe)
  23. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  24. Springer Nature
  25. Wikidata
  26. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
    alpha-glycerophosphoric acid
    https://www.ncbi.nlm.nih.gov/mesh/67029620
  27. PubChem
  28. Glycan Naming and Subsumption Ontology (GNOme)
    GNOme
  29. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  30. PATENTSCOPE (WIPO)
CONTENTS