MiMeDB: Showing metabocard for 1D-myo-inositol 3-phosphate (MMDBc0054151)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:08 UTC

Update Date

2025-10-07 16:08:23 UTC

Metabolite ID

MMDBc0054151

Metabolite Identification

Common Name

1D-myo-inositol 3-phosphate

Description

1D-myo-inositol 3-phosphate is a polyol and a member of the inositol phosphate class, which plays a crucial role in various cellular signaling pathways. Chemically, it is characterized by a six-carbon sugar structure with multiple hydroxyl groups, specifically phosphorylated at the 3-position, contributing to its reactivity and involvement in metabolic processes. It serves as a precursor in the biosynthesis of inositol phosphates and is generated from myo-inositol through the action of the enzyme 1D-myo-inositol 3-phosphate synthase (EC 5.5.1.4), which catalyzes the first step in myo-inositol biosynthesis and directs phytic acid biosynthesis in seeds (PMID:19021878 ). Additionally, 1D-myo-inositol 3-phosphate is implicated in lipid metabolism, as evidenced by its association with 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI(3)P) levels under specific conditions (PMID:37315361 ). It is also involved in a phosphorylation pathway that operates independently of inositol lipids, highlighting its versatility in cellular signaling (PMID:17961936 ). The structural characterization of its complexes, such as with the TK2285 protein, further elucidates its biochemical interactions (PMID:25972008 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231220522D          

 16 16  0  0  1  0            999 V2000
   13.3911   -3.0502    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.6766   -3.4627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1056   -4.2877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2476   -4.2877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1056   -5.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2476   -5.9378    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6766   -6.7628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1056   -2.6377    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9786   -2.3357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8036   -3.7646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6766   -4.2877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3911   -4.7002    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9622   -4.7002    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.3911   -5.5253    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9622   -5.5253    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6766   -5.9378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  2  0  0  0  0
  2 11  1  0  0  0  0
 12  3  1  1  0  0  0
 13  4  1  6  0  0  0
 14  5  1  1  0  0  0
 15  6  1  1  0  0  0
  7 16  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054151

> <DATABASE_NAME>
MIME

> <SMILES>
OC1[C@H](O)[C@H](O)C(OP(O)(O)=O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13O9P/c7-1-2(8)4(10)6(5(11)3(1)9)15-16(12,13)14/h1-11H,(H2,12,13,14)/t1?,2-,3+,4-,5-,6?/m0/s1

> <INCHI_KEY>
INAPMGSXUVUWAF-LXOASSSBSA-N

> <FORMULA>
C6H13O9P

> <MOLECULAR_WEIGHT>
260.1358

> <EXACT_MASS>
260.029718526

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
20.647787993272374

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-3.9055756833333333

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.19411178891901

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1625722061585537

> <JCHEM_PKA_STRONGEST_BASIC>
-3.645813019693807

> <JCHEM_POLAR_SURFACE_AREA>
167.91

> <JCHEM_REFRACTIVITY>
46.64789999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.95e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      24.997  -5.694   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      23.663  -6.464   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      26.330  -8.004   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      20.996  -8.004   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      26.330 -11.084   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      20.996 -11.084   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      23.663 -12.624   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      26.330  -4.924   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      24.227  -4.360   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      25.767  -7.027   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      23.663  -8.004   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.997  -8.774   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.329  -8.774   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      24.997 -10.314   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.329 -10.314   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      23.663 -11.084   0.000  0.00  0.00           C+0
CONECT    1    2    8    9   10                                             
CONECT    2    1   11                                                       
CONECT    3   12                                                            
CONECT    4   13                                                            
CONECT    5   14                                                            
CONECT    6   15                                                            
CONECT    7   16                                                            
CONECT    8    1                                                            
CONECT    9    1                                                            
CONECT   10    1                                                            
CONECT   11    2   12   13                                                  
CONECT   12    3   11   14                                                  
CONECT   13    4   11   15                                                  
CONECT   14    5   12   16                                                  
CONECT   15    6   13   16                                                  
CONECT   16    7   14   15                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

Synonyms

Value	Source
1D-Myo-inositol 3-phosphoric acid	Generator
1D-Myo-inositol 3-monophosphate	HMDB
1l-Myo-inositol 1-phosphate	HMDB
D-Myo-inositol 3-monophosphate	HMDB
D-Myo-inositol 3-phosphate	HMDB
Inositol 3-monophosphate	HMDB
Inositol 3-phosphate	HMDB
L-Myo-inositol 1-phosphate	HMDB
Myo-inositol 3-monophosphate	HMDB
Myo-inositol 3-phosphate	HMDB
D-Myo-inositol-3-phosphate	HMDB
Inositol 3-phosphate, (-)-isomer	HMDB
Myoinositol 3-phosphate	HMDB

Molecular Formula

C₆H₁₃O₉P

Average Mass

260.1358

Monoisotopic Mass

260.029718526

IUPAC Name

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

Traditional Name

[(2S,3R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OC1[C@H](O)[C@H](O)C(OP(O)(O)=O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H13O9P/c7-1-2(8)4(10)6(5(11)3(1)9)15-16(12,13)14/h1-11H,(H2,12,13,14)/t1?,2-,3+,4-,5-,6?/m0/s1

InChI Key

INAPMGSXUVUWAF-LXOASSSBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as inositol phosphates. Inositol phosphates are compounds containing a phosphate group attached to an inositol (or cyclohexanehexol) moiety.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Inositol phosphates

Alternative Parents

Substituents

Inositol phosphate
Monoalkyl phosphate
Cyclohexanol
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	39.5 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.9	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	167.91 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	46.65 m³·mol⁻¹	ChemAxon
Polarizability	20.65 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	splash10-0005-9650000000-8feb65965bdf1456b458	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-0a4i-2293126000-549eada55b744fac8622	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-3290000000-43552f3f7fc8310bd494	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-2190000000-c67e077835114485af8b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9500000000-f36378811541baf7cfef	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-4090000000-01afb15b24735a3a5165	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9110000000-02799b91b498522af46d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b3dde662ddcb72b87b4e	2017-09-01	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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
MMDBr0020004	1D-Myo-inositol 3,4-bisphosphate	1D-myo-inositol 3-phosphate	Unknown Protein		PathBank	31602464
MMDBr0020005	1D-myo-inositol 3-phosphate	myo-Inositol	Inositol monophosphatase 1	Dephosphorylation	PathBank	31602464
MMDBr0020006	Glucose 6-phosphate	1D-myo-inositol 3-phosphate	Unknown Protein		PathBank	31602464
MMDBr0025728	1D-myo-inositol 3-phosphate	CMP	Phosphatidylinositol phosphate synthase	Synthesis	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
Eukaryota/Fungi	Ascomycota	4	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Actinobacteria	71	Human ; Human feces; Cattle
Bacteria/Eubacteria	Aquificae	1
Archaea/Archaea	Euryarchaeota	5
Bacteria	Proteobacteria	1
Archaea/Archaea	Crenarchaeota	1
Archaea	Crenarchaeota	1

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

HMDB0006814

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB024095

KNApSAcK ID

Not Available

Chemspider ID

389182

KEGG Compound ID

C04006

BioCyc ID

Not Available

BiGG ID

42948

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440194

PDB ID

Not Available

ChEBI ID

18169

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 1D-myo-inositol 3-phosphate (MMDBc0054151)

MOL for #<Metabolite:0x00007fade12c1be0>

3D MOL for #<Metabolite:0x00007fade12c1be0>

3D SDF for #<Metabolite:0x00007fade12c1be0>

3D-SDF for #<Metabolite:0x00007fade12c1be0>

PDB for #<Metabolite:0x00007fade12c1be0>

3D PDB for #<Metabolite:0x00007fade12c1be0>

SMILES for #<Metabolite:0x00007fade12c1be0>

INCHI for #<Metabolite:0x00007fade12c1be0>

Structure for #<Metabolite:0x00007fade12c1be0>

3D Structure for #<Metabolite:0x00007fade12c1be0>