MiMeDB: Showing metabocard for 1-Phosphatidyl-1D-myo-inositol 3-phosphate (MMDBc0047786)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:42:34 UTC

Update Date

2024-04-30 20:30:15 UTC

Metabolite ID

MMDBc0047786

Metabolite Identification

Common Name

1-Phosphatidyl-1D-myo-inositol 3-phosphate

Description

1-Phosphatidyl-1D-myo-inositol 3-phosphate is a substrate for FYVE finger-containing phosphoinositide kinase and Neutrophil cytosol factor 4.

Structure

MOL SDF PDB SMILES InChI

HMDB03850.mol
  Mrv0541 02231219482D          

 29 29  0  0  0  0            999 V2000
   -1.7318   -0.8227    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7341   -1.6477    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0208   -2.0622    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3052   -1.6517    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3028   -0.8267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0162   -0.4122    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0162    0.4128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4463   -0.4102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4093   -2.0642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4116   -0.4142    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0208   -2.8872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3011    0.8257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7126    1.5385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1124    0.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4134    1.2382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4134    2.0601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303    2.4741    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8472    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5604    2.4720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2755    2.0591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5604    3.2963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303    3.2963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8460    3.7095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4170    3.7081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -2.8845    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -2.8845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6255   -2.8845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -3.7095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  6  7  1  1  0  0  0
  1  8  1  1  0  0  0
  2  9  1  1  0  0  0
  4 10  1  1  0  0  0
  5 11  1  6  0  0  0
  3 12  1  6  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 18 23  1  6  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
  9 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 26 29  1  0  0  0  0
M  END

HMDB03850.mol
  Mrv0541 02231219482D          

 29 29  0  0  0  0            999 V2000
   -1.7318   -0.8227    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7341   -1.6477    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0208   -2.0622    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3052   -1.6517    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3028   -0.8267    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0162   -0.4122    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0162    0.4128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4463   -0.4102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4093   -2.0642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4116   -0.4142    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0208   -2.8872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3011    0.8257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7126    1.5385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1124    0.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4134    1.2382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4134    2.0601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303    2.4741    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8472    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5604    2.4720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2755    2.0591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5604    3.2963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1303    3.2963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8460    3.7095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4170    3.7081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -2.8845    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -2.8845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6255   -2.8845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4486   -3.7095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  6  7  1  1  0  0  0
  1  8  1  1  0  0  0
  2  9  1  1  0  0  0
  4 10  1  1  0  0  0
  5 11  1  6  0  0  0
  3 12  1  6  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 18 23  1  6  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
  9 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 26 29  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047786

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H20O16P2/c12-4(13)1-3(11(18)19)2-25-29(23,24)27-10-7(16)5(14)6(15)9(8(10)17)26-28(20,21)22/h3,5-10,14-17H,1-2H2,(H,12,13)(H,18,19)(H,23,24)(H2,20,21,22)/t3-,5+,6+,7-,8-,9-,10+/m1/s1

> <INCHI_KEY>
YKMGQFUXYYTRLF-SLJXNWFNSA-N

> <FORMULA>
C11H20O16P2

> <MOLECULAR_WEIGHT>
470.2144

> <EXACT_MASS>
470.022657616

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
36.848168915455624

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-({[hydroxy({[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy})phosphoryl]oxy}methyl)butanedioic acid

> <ALOGPS_LOGP>
-1.58

> <JCHEM_LOGP>
-4.268871769

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.9232796866669712

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0773571014398016

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6669494517647445

> <JCHEM_POLAR_SURFACE_AREA>
278.03999999999996

> <JCHEM_REFRACTIVITY>
83.62799999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.42e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[({hydroxy[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxyphosphoryl}oxy)methyl]butanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: HMDB03850.mol                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -3.233  -1.536   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.237  -3.076   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.905  -3.849   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.570  -3.083   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.565  -1.543   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.897  -0.769   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.897   0.771   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -4.566  -0.766   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.571  -3.846   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.764  -3.853   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.768  -0.773   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.905  -5.389   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -0.562   1.541   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -1.330   2.872   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.210   0.204   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.772   2.311   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.772   3.846   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.110   4.618   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.448   3.846   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.779   4.614   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.114   3.844   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.779   6.153   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.110   6.153   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.446   6.924   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.778   6.922   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      -4.571  -5.384   0.000  0.00  0.00           P+0
HETATM   27  O   UNK     0      -6.114  -5.384   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -3.034  -5.384   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -4.571  -6.924   0.000  0.00  0.00           O+0
CONECT    1    2    6    8                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6   13                                                       
CONECT    8    1                                                            
CONECT    9    2   26                                                       
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    3                                                            
CONECT   13    7   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   18   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26    9   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   58    0
END

Synonyms

Value	Source
1-Phosphatidyl-1D-myo-inositol 3-phosphoric acid	Generator
Phosphatidylinositol 3-phosphate	HMDB
PtdINS3p	HMDB
Phosphatidylinositol 3-monophosphate	HMDB

Molecular Formula

C₁₁H₂₀O₁₆P₂

Average Mass

470.2144

Monoisotopic Mass

470.022657616

IUPAC Name

(2R)-2-({[hydroxy({[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy})phosphoryl]oxy}methyl)butanedioic acid

Traditional Name

(2R)-2-[({hydroxy[(1S,2R,3S,4S,5R,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxyphosphoryl}oxy)methyl]butanedioic acid

CAS Registry Number

Not Available

SMILES

O[C@H]1[C@H](O)[C@@H](OP(O)(O)=O)[C@@H](O)[C@@H](OP(O)(=O)OC[C@@H](CC(O)=O)C(O)=O)[C@@H]1O

InChI Identifier

InChI=1S/C11H20O16P2/c12-4(13)1-3(11(18)19)2-25-29(23,24)27-10-7(16)5(14)6(15)9(8(10)17)26-28(20,21)22/h3,5-10,14-17H,1-2H2,(H,12,13)(H,18,19)(H,23,24)(H2,20,21,22)/t3-,5+,6+,7-,8-,9-,10+/m1/s1

InChI Key

YKMGQFUXYYTRLF-SLJXNWFNSA-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
Cyclohexanol
Monoalkyl phosphate
Dialkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Dicarboxylic acid or derivatives
Fatty acid
Secondary alcohol
Polyol
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Organic oxide
Hydrocarbon derivative
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	24.2 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-4.3	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.08	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	278.04 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	83.63 m³·mol⁻¹	ChemAxon
Polarizability	36.85 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	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	splash10-0002-9435800000-20b98725dd32a066ce96	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00di-4171439000-170048f5603381abd85d	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0un9-2321900000-465a728b8ebbd4c60bc4	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0019-9801100000-f7ed730835b2177c3826	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0012-8920000000-bdd0ea1a0d8a052bd271	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00p0-3014900000-487db5edd9cc11fd0104	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9214300000-da55c482aa9497a13016	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-1b9fc39dc0e9a82537c0	2016-09-14	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Skeletal Muscle

Tissue Locations

Skeletal Muscle

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

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

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
Human Feces	Detected but not Quantified									HMDB
Human Skeletal muscle	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0003850

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023237

KNApSAcK ID

Not Available

Chemspider ID

5256742

KEGG Compound ID

C04549

BioCyc ID

Not Available

BiGG ID

44024

Wikipedia Link

Not Available

METLIN ID

6985

PubChem Compound

6857403

PDB ID

Not Available

ChEBI ID

17283

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Buj-Bello A, Furling D, Tronchere H, Laporte J, Lerouge T, Butler-Browne GS, Mandel JL: Muscle-specific alternative splicing of myotubularin-related 1 gene is impaired in DM1 muscle cells. Hum Mol Genet. 2002 Sep 15;11(19):2297-307. doi: 10.1093/hmg/11.19.2297. [PubMed:12217958 ]

Showing metabocard for 1-Phosphatidyl-1D-myo-inositol 3-phosphate (MMDBc0047786)

MOL for #<Metabolite:0x00007fecd2573cc8>

3D MOL for #<Metabolite:0x00007fecd2573cc8>

3D SDF for #<Metabolite:0x00007fecd2573cc8>

3D-SDF for #<Metabolite:0x00007fecd2573cc8>

PDB for #<Metabolite:0x00007fecd2573cc8>

3D PDB for #<Metabolite:0x00007fecd2573cc8>

SMILES for #<Metabolite:0x00007fecd2573cc8>

INCHI for #<Metabolite:0x00007fecd2573cc8>

Structure for #<Metabolite:0x00007fecd2573cc8>

3D Structure for #<Metabolite:0x00007fecd2573cc8>