MiMeDB: Showing metabocard for 1-(sn-glycero-3-phospho)-1D-myo-inositol (MMDBc0033124)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:35:45 UTC

Update Date

2022-08-31 22:26:28 UTC

Metabolite ID

MMDBc0033124

Metabolite Identification

Common Name

1-(sn-glycero-3-phospho)-1D-myo-inositol

Description

1-(sn-glycero-3-phospho)-1D-myo-inositol belongs to the class of organic compounds known as glycerophosphoinositols. These are lipids containing a glycerol moiety carrying a phosphoinositol at the 3-position. 1-(sn-glycero-3-phospho)-1D-myo-inositol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222362D          

 22 22  0  0  0  0            999 V2000
   -0.9332   -0.1187    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6477    0.2938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2187    0.2938    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4957   -0.1187    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2102    0.2938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4957   -0.9438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2102   -1.3563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2187   -1.3563    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2187   -2.1813    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332   -0.9438    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6477   -1.3563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2187    1.1188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    2.3563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    1.5313    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    0.7063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7582    1.5313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4727    1.9438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4727    3.5938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7582    4.0063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6477    2.7688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4727    2.7688    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2977    2.7688    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  4  1  0  0  0  0
  1 10  1  0  0  0  0
 10  8  1  0  0  0  0
  8  6  1  0  0  0  0
  6  4  1  0  0  0  0
  1  2  1  1  0  0  0
  3 12  1  1  0  0  0
  4  5  1  6  0  0  0
  6  7  1  1  0  0  0
  8  9  1  6  0  0  0
 10 11  1  1  0  0  0
 12 14  1  0  0  0  0
 14 13  2  0  0  0  0
 14 16  1  0  0  0  0
 14 15  1  0  0  0  0
 16 17  1  0  0  0  0
 17 21  1  0  0  0  0
 21 18  1  0  0  0  0
 18 19  1  0  0  0  0
 21 20  1  1  0  0  0
 21 22  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033124

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(CO)COP(O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H19O11P/c10-1-3(11)2-19-21(17,18)20-9-7(15)5(13)4(12)6(14)8(9)16/h3-16H,1-2H2,(H,17,18)/t3-,4-,5-,6+,7+,8+,9-/m0/s1

> <INCHI_KEY>
BMVUIWJCUQSHLZ-HVVSXIBASA-N

> <FORMULA>
C9H19O11P

> <MOLECULAR_WEIGHT>
334.2143

> <EXACT_MASS>
334.066497962

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
28.672438907216907

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2,3-dihydroxypropoxy]({[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-2.49

> <JCHEM_LOGP>
-4.848051914666666

> <ALOGPS_LOGS>
-0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.338351990720948

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8335431742771062

> <JCHEM_PKA_STRONGEST_BASIC>
-2.968964768452052

> <JCHEM_POLAR_SURFACE_AREA>
197.36999999999998

> <JCHEM_REFRACTIVITY>
63.385000000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,3-dihydroxypropoxy[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxyphosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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      -1.742  -0.222   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.076   0.548   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.408   0.548   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.925  -0.222   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.259   0.548   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.925  -1.762   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.259  -2.532   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.408  -2.532   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.408  -4.072   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.742  -1.762   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.076  -2.532   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.408   2.088   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.742   4.398   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      -1.742   2.858   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      -1.742   1.318   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -3.282   2.858   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.616   3.628   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.616   6.708   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.282   7.478   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -3.076   5.168   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -4.616   5.168   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0      -6.156   5.168   0.000  0.00  0.00           H+0
CONECT    1    3   10    2                                                  
CONECT    2    1                                                            
CONECT    3    1    4   12                                                  
CONECT    4    3    6    5                                                  
CONECT    5    4                                                            
CONECT    6    8    4    7                                                  
CONECT    7    6                                                            
CONECT    8   10    6    9                                                  
CONECT    9    8                                                            
CONECT   10    1    8   11                                                  
CONECT   11   10                                                            
CONECT   12    3   14                                                       
CONECT   13   14                                                            
CONECT   14   12   13   16   15                                             
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   21                                                       
CONECT   18   21   19                                                       
CONECT   19   18                                                            
CONECT   20   21                                                            
CONECT   21   17   18   20   22                                             
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₉O₁₁P

Average Mass

334.2143

Monoisotopic Mass

334.066497962

IUPAC Name

[(2S)-2,3-dihydroxypropoxy]({[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy})phosphinic acid

Traditional Name

(2S)-2,3-dihydroxypropoxy[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxyphosphinic acid

CAS Registry Number

Not Available

SMILES

[H][C@](O)(CO)COP(O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C9H19O11P/c10-1-3(11)2-19-21(17,18)20-9-7(15)5(13)4(12)6(14)8(9)16/h3-16H,1-2H2,(H,17,18)/t3-,4-,5-,6+,7+,8+,9-/m0/s1

InChI Key

BMVUIWJCUQSHLZ-HVVSXIBASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerophosphoinositols. These are lipids containing a glycerol moiety carrying a phosphoinositol at the 3-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoinositols

Direct Parent

Glycerophosphoinositols

Alternative Parents

Substituents

Glycerophosphoinositol
Inositol phosphate
Dialkyl phosphate
Cyclohexanol
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Cyclitol or derivatives
Cyclic alcohol
Secondary alcohol
Polyol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	40.9 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-4.8	ChemAxon
logS	-0.91	ALOGPS
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	197.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	63.38 m³·mol⁻¹	ChemAxon
Polarizability	28.67 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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	splash10-02t9-5497000000-71befcc2c86295c3ce7f	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00tr-5729000000-1bcc5d7b9e5d29ea58aa	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-9232000000-cab2d9b4f775d3a32831	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06tb-9500000000-a623a4c7cd6c19b4ffe7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1139000000-46b346ec24fd0486938a	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-056r-9583000000-ab05542eabc555d149cc	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-7c0c1f290d5af79453e4	2016-09-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0010697	1-(sn-glycero-3-phospho)-1D-myo-inositol	Glycerol	annexin A3		VMH; KEGG	30371894
MMDBr0010698	1-(sn-glycero-3-phospho)-1D-myo-inositol	Glycerol 3-phosphate	glycerophosphodiester phosphodiesterase 1		VMH; KEGG	30371894

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

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 1-(sn-glycero-3-phospho)-1D-myo-inositol (MMDBc0033124)

MOL for #<Metabolite:0x00007fdb2c428790>

3D MOL for #<Metabolite:0x00007fdb2c428790>

3D SDF for #<Metabolite:0x00007fdb2c428790>

3D-SDF for #<Metabolite:0x00007fdb2c428790>

PDB for #<Metabolite:0x00007fdb2c428790>

3D PDB for #<Metabolite:0x00007fdb2c428790>

SMILES for #<Metabolite:0x00007fdb2c428790>

INCHI for #<Metabolite:0x00007fdb2c428790>

Structure for #<Metabolite:0x00007fdb2c428790>

3D Structure for #<Metabolite:0x00007fdb2c428790>