MiMeDB: Showing metabocard for 1,2-Didecanoyl-sn-glycero-3-phosphate (MMDBc0057200)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-11-09 20:27:12 UTC

Update Date

2025-10-07 16:09:56 UTC

Metabolite ID

MMDBc0057200

Metabolite Identification

Common Name

1,2-Didecanoyl-sn-glycero-3-phosphate

Description

1,2-Didecanoyl-sn-glycero-3-phosphate is a phospholipid belonging to the class of glycerophospholipids. Its chemical structure features a glycerol backbone esterified with two decanoyl fatty acid chains at the sn-1 and sn-2 positions, and a phosphate group at the sn-3 position. This unique arrangement contributes to its amphiphilic properties, making it an important component in various biological membranes and lipid bilayers. In biochemical pathways, 1,2-didecanoyl-sn-glycero-3-phosphate can participate in the formation of liposomes and lipid nanoparticles, which are utilized for drug delivery systems. For instance, anionic lipid 1,2-didecanoyl-sn-glycero-3-phosphate (sodium salt) was incorporated into an ionic complex with cationic N α-deoxycholyl-l-lysyl-methylester to enhance oral bioavailability in a study, yielding a formulation referred to as ELNE#7 (PMID:33107339 ). This highlights its role in pharmaceutical applications, particularly in improving the delivery and efficacy of therapeutic agents.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041413242D          

 33 32  0  0  1  0            999 V2000
   -8.0289   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4039   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6894   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6000   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9749   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8855   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2605   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1711   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5460   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4566   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8315   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7421   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1171   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0276   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4026   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3132   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5447   -5.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5447   -4.2868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5987   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5987   -3.0493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737   -5.1118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -6.3493    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0842   -6.3493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -7.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -5.5243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -3.8743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -6.3493    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698   -4.6993    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
 22 17  1  0  0  0  0
 23 18  1  0  0  0  0
 24 22  2  0  0  0  0
 25 23  2  0  0  0  0
 29 19  1  0  0  0  0
 29 22  1  0  0  0  0
 30 20  1  0  0  0  0
 21 31  1  6  0  0  0
 31 23  1  0  0  0  0
 32 26  1  0  0  0  0
 32 27  1  0  0  0  0
 32 28  2  0  0  0  0
 32 30  1  0  0  0  0
 21 33  1  6  0  0  0
M  CHG  1  26  -1
M  END


  Mrv0541 05041413242D          

 33 32  0  0  1  0            999 V2000
   -8.0289   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4039   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6894   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6000   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9749   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8855   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2605   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1711   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5460   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4566   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8315   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7421   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1171   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0276   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4026   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3132   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5447   -5.1118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5447   -4.2868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5987   -3.8743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5987   -3.0493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737   -5.1118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -6.3493    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0842   -6.3493    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -7.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -5.5243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -3.8743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2592   -6.3493    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698   -4.6993    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
 22 17  1  0  0  0  0
 23 18  1  0  0  0  0
 24 22  2  0  0  0  0
 25 23  2  0  0  0  0
 29 19  1  0  0  0  0
 29 22  1  0  0  0  0
 30 20  1  0  0  0  0
 21 31  1  6  0  0  0
 31 23  1  0  0  0  0
 32 26  1  0  0  0  0
 32 27  1  0  0  0  0
 32 28  2  0  0  0  0
 32 30  1  0  0  0  0
 21 33  1  6  0  0  0
M  CHG  1  26  -1
M  END
> <DATABASE_ID>
MMDBc0057200

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C23H45O8P/c1-3-5-7-9-11-13-15-17-22(24)29-19-21(20-30-32(26,27)28)31-23(25)18-16-14-12-10-8-6-4-2/h21H,3-20H2,1-2H3,(H2,26,27,28)/p-1/t21-/m1/s1

> <INCHI_KEY>
PHQFPHNJHDEXLJ-OAQYLSRUSA-M

> <FORMULA>
C23H44O8P

> <MOLECULAR_WEIGHT>
479.5644

> <EXACT_MASS>
479.277379896

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
53.90068684789094

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-1-(decanoyloxy)-3-(hydrogen phosphonatooxy)propan-2-yl decanoate

> <ALOGPS_LOGP>
5.27

> <JCHEM_LOGP>
6.544703770666665

> <ALOGPS_LOGS>
-5.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.343234649149876

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3174060830586427

> <JCHEM_PKA_STRONGEST_BASIC>
-6.744159310865148

> <JCHEM_POLAR_SURFACE_AREA>
122.19000000000001

> <JCHEM_REFRACTIVITY>
122.23809999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-1-(decanoyloxy)-3-(hydrogen phosphonatooxy)propan-2-yl decanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   33  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8   12                                                       
CONECT   11    9   13                                                       
CONECT   12   10   14                                                       
CONECT   13   11   15                                                       
CONECT   14   12   16                                                       
CONECT   15   13   17                                                       
CONECT   16   14   18                                                       
CONECT   17   15   22                                                       
CONECT   18   16   23                                                       
CONECT   19   21   29                                                       
CONECT   20   21   30                                                       
CONECT   21   19   20   31   33                                             
CONECT   22   17   24   29                                                  
CONECT   23   18   25   31                                                  
CONECT   24   22                                                            
CONECT   25   23                                                            
CONECT   26   32                                                            
CONECT   27   32                                                            
CONECT   28   32                                                            
CONECT   29   19   22                                                       
CONECT   30   20   32                                                       
CONECT   31   21   23                                                       
CONECT   32   26   27   28   30                                             
CONECT   33   21                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   64    0
END

Synonyms

Value	Source
(2R)-1-(Decanoyloxy)-3-(hydrogen phosphonatooxy)propan-2-yl decanoic acid	Generator

Molecular Formula

C₂₃H₄₄O₈P

Average Mass

479.5644

Monoisotopic Mass

479.277379896

IUPAC Name

(2R)-1-(decanoyloxy)-3-(hydrogen phosphonatooxy)propan-2-yl decanoate

Traditional Name

(2R)-1-(decanoyloxy)-3-(hydrogen phosphonatooxy)propan-2-yl decanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C23H45O8P/c1-3-5-7-9-11-13-15-17-22(24)29-19-21(20-30-32(26,27)28)31-23(25)18-16-14-12-10-8-6-4-2/h21H,3-20H2,1-2H3,(H2,26,27,28)/p-1/t21-/m1/s1

InChI Key

PHQFPHNJHDEXLJ-OAQYLSRUSA-M

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.0018 g/L	ALOGPS
logP	5.27	ALOGPS
logP	6.54	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	1.32	ChemAxon
pKa (Strongest Basic)	-6.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	122.19 Å²	ChemAxon
Rotatable Bond Count	24	ChemAxon
Refractivity	122.24 m³·mol⁻¹	ChemAxon
Polarizability	53.9 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

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

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

49867860

PDB ID

XPA

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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 1,2-Didecanoyl-sn-glycero-3-phosphate (MMDBc0057200)

MOL for #<Metabolite:0x00007f8dd1527928>

3D MOL for #<Metabolite:0x00007f8dd1527928>

3D SDF for #<Metabolite:0x00007f8dd1527928>

3D-SDF for #<Metabolite:0x00007f8dd1527928>

PDB for #<Metabolite:0x00007f8dd1527928>

3D PDB for #<Metabolite:0x00007f8dd1527928>

SMILES for #<Metabolite:0x00007f8dd1527928>

INCHI for #<Metabolite:0x00007f8dd1527928>

Structure for #<Metabolite:0x00007f8dd1527928>

3D Structure for #<Metabolite:0x00007f8dd1527928>