MiMeDB: Showing metabocard for Phosphatidylglycerophosphate (MMDBc0031726)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:45:59 UTC

Update Date

2022-08-31 18:23:58 UTC

Metabolite ID

MMDBc0031726

Metabolite Identification

Common Name

Phosphatidylglycerophosphate

Description

Phosphatidylglycerophosphate belongs to the class of Phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08151207492D          

 25 24  0  0  0  0            999 V2000
   -3.7125    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875    3.5724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7750    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500    5.1118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500    3.4618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250    4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9500    4.2868    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3000    2.8579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
  7 11  1  1  0  0  0
 17  3  1  0  0  0  0
 17  5  1  0  0  0  0
 18  6  1  0  0  0  0
  8 18  1  6  0  0  0
 19  1  1  0  0  0  0
 20  2  1  0  0  0  0
 21  4  1  0  0  0  0
 22 12  1  0  0  0  0
 22 13  1  0  0  0  0
 22 14  2  0  0  0  0
 22 19  1  0  0  0  0
 23 15  1  0  0  0  0
 23 16  2  0  0  0  0
 23 20  1  0  0  0  0
 23 21  1  0  0  0  0
  7 24  1  1  0  0  0
  8 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031726

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC=O)OC=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16O13P2/c9-5-17-3-8(18-6-10)4-21-23(15,16)20-2-7(11)1-19-22(12,13)14/h5-8,11H,1-4H2,(H,15,16)(H2,12,13,14)/t7-,8+/m0/s1

> <INCHI_KEY>
ZSPJCYNIVYENCI-JGVFFNPUSA-N

> <FORMULA>
C8H16O13P2

> <MOLECULAR_WEIGHT>
382.1524

> <EXACT_MASS>
382.006613622

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
29.345532830523126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-3-({[(2R)-2,3-bis(formyloxy)propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-2.2437689119999997

> <ALOGPS_LOGS>
-1.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.0402072854726705

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.354879766971247

> <JCHEM_PKA_STRONGEST_BASIC>
-3.410499386302641

> <JCHEM_POLAR_SURFACE_AREA>
195.34999999999994

> <JCHEM_REFRACTIVITY>
68.32100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.66e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-{[(2R)-2,3-bis(formyloxy)propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   23  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    7   19                                                       
CONECT    2    7   20                                                       
CONECT    3    8   17                                                       
CONECT    4    8   21                                                       
CONECT    5    9   17                                                       
CONECT    6   10   18                                                       
CONECT    7    1    2   11   24                                             
CONECT    8    3    4   18   25                                             
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12   22                                                            
CONECT   13   22                                                            
CONECT   14   22                                                            
CONECT   15   23                                                            
CONECT   16   23                                                            
CONECT   17    3    5                                                       
CONECT   18    6    8                                                       
CONECT   19    1   22                                                       
CONECT   20    2   23                                                       
CONECT   21    4   23                                                       
CONECT   22   12   13   14   19                                             
CONECT   23   15   16   20   21                                             
CONECT   24    7                                                            
CONECT   25    8                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   48    0
END

Synonyms

Value	Source
Phosphatidylglycerophosphoric acid	Generator

Molecular Formula

C₈H₁₆O₁₃P₂

Average Mass

382.1524

Monoisotopic Mass

382.006613622

IUPAC Name

[(2S)-3-({[(2R)-2,3-bis(formyloxy)propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

Traditional Name

(2S)-3-{[(2R)-2,3-bis(formyloxy)propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC=O)OC=O

InChI Identifier

InChI=1S/C8H16O13P2/c9-5-17-3-8(18-6-10)4-21-23(15,16)20-2-7(11)1-19-22(12,13)14/h5-8,11H,1-4H2,(H,15,16)(H2,12,13,14)/t7-,8+/m0/s1

InChI Key

ZSPJCYNIVYENCI-JGVFFNPUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoglycerophosphates

Direct Parent

Phosphatidylglycerophosphates

Alternative Parents

Substituents

Diacylglycerophosphoglycerophosphate
Sn-glycerol-3-phosphate
Dialkyl phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.66 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-2.2	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.35	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	195.35 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	68.32 m³·mol⁻¹	ChemAxon
Polarizability	29.35 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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

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
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46873832

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14. doi: 10.1093/nar/gkr988. Epub 2011 Nov 10. [PubMed:22080510 ]

Showing metabocard for Phosphatidylglycerophosphate (MMDBc0031726)

MOL for #<Metabolite:0x00007f1240761d40>

3D MOL for #<Metabolite:0x00007f1240761d40>

3D SDF for #<Metabolite:0x00007f1240761d40>

3D-SDF for #<Metabolite:0x00007f1240761d40>

PDB for #<Metabolite:0x00007f1240761d40>

3D PDB for #<Metabolite:0x00007f1240761d40>

SMILES for #<Metabolite:0x00007f1240761d40>

INCHI for #<Metabolite:0x00007f1240761d40>

Structure for #<Metabolite:0x00007f1240761d40>

3D Structure for #<Metabolite:0x00007f1240761d40>