MiMeDB: Showing metabocard for sn-3-O-(geranylgeranyl)glycerol 1-phosphate (MMDBc0054664)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:23:21 UTC

Update Date

2022-08-12 20:09:02 UTC

Metabolite ID

MMDBc0054664

Metabolite Identification

Common Name

sn-3-O-(geranylgeranyl)glycerol 1-phosphate

Description

sn-3-O-(geranylgeranyl)glycerol 1-phosphate belongs to the class of organic compounds known as acyclic diterpenoids. These are diterpenoids (compounds made of four consecutive isoprene units) that do not contain a cycle. sn-3-O-(geranylgeranyl)glycerol 1-phosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041521292D          
 
 30 29  0  0  1  0            999 V2000
   22.9370   -8.2170    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   22.9407   -9.0446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.1131   -8.2207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9370   -7.3931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7607   -8.2170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9407   -9.8685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2269  -10.2823    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.2269  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5132   -9.8685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.5132  -11.5200    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7956  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0819  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3643  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6506  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3643  -10.2823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9368  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2192  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5055  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7955  -11.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5055  -10.2823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7917  -12.3857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3991  -12.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4067  -13.6424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1244  -14.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6930  -14.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1319  -14.8763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8495  -15.2825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -16.1064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5746  -16.5164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1433  -16.5240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
M  END

 
  Mrv1533006041521292D          
 
 30 29  0  0  1  0            999 V2000
   22.9370   -8.2170    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   22.9407   -9.0446    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.1131   -8.2207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9370   -7.3931    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7607   -8.2170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9407   -9.8685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2269  -10.2823    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.2269  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5132   -9.8685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.5132  -11.5200    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7956  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0819  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3643  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6506  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3643  -10.2823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9368  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2192  -11.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5055  -11.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7955  -11.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5055  -10.2823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7917  -12.3857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3991  -12.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4067  -13.6424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1244  -14.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6930  -14.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1319  -14.8763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8495  -15.2825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8532  -16.1064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5746  -16.5164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1433  -16.5240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054664

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COC[C@H](O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H41O6P/c1-19(2)9-6-10-20(3)11-7-12-21(4)13-8-14-22(5)15-16-28-17-23(24)18-29-30(25,26)27/h9,11,13,15,23-24H,6-8,10,12,14,16-18H2,1-5H3,(H2,25,26,27)/b20-11+,21-13+,22-15+/t23-/m0/s1

> <INCHI_KEY>
BJLPWUCPFAJINB-UAQSTNRTSA-N

> <FORMULA>
C23H41O6P

> <MOLECULAR_WEIGHT>
444.549

> <EXACT_MASS>
444.264076038

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
50.80805565427244

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-{[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]oxy}propoxy]phosphonic acid

> <ALOGPS_LOGP>
4.33

> <JCHEM_LOGP>
5.020935364333334

> <ALOGPS_LOGS>
-5.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.532781306916074

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5069848404295634

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3935261977748485

> <JCHEM_POLAR_SURFACE_AREA>
96.22

> <JCHEM_REFRACTIVITY>
126.66619999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.09e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  P   UNK     0      42.816 -15.338   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      42.823 -16.883   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      41.278 -15.345   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      42.816 -13.800   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      44.353 -15.338   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      42.823 -18.421   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      41.490 -19.194   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      41.490 -20.731   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      40.158 -18.421   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      40.158 -21.504   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      38.818 -20.731   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      37.486 -21.504   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.147 -20.731   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      34.814 -21.504   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      36.147 -19.194   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.482 -20.731   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      32.143 -21.504   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      30.810 -20.731   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      29.485 -21.490   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      30.810 -19.194   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      29.478 -23.120   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      30.612 -23.921   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      30.626 -25.466   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      31.965 -26.224   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      29.294 -26.245   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      31.980 -27.769   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      33.319 -28.527   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      33.326 -30.065   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      34.673 -30.831   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      32.001 -30.845   0.000  0.00  0.00           C+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10                                                       
CONECT    9    7                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13   16                                                       
CONECT   15   13                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18   21                                                       
CONECT   20   18                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23   26                                                       
CONECT   25   23                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   58    0
END

Synonyms

Value	Source
sn-3-O-(Geranylgeranyl)glycerol 1-phosphoric acid	Generator

Molecular Formula

C₂₃H₄₁O₆P

Average Mass

444.549

Monoisotopic Mass

444.264076038

IUPAC Name

[(2S)-2-hydroxy-3-{[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]oxy}propoxy]phosphonic acid

Traditional Name

(2S)-2-hydroxy-3-{[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]oxy}propoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C(C)=C\COC[C@H](O)COP(O)(O)=O

InChI Identifier

InChI=1S/C23H41O6P/c1-19(2)9-6-10-20(3)11-7-12-21(4)13-8-14-22(5)15-16-28-17-23(24)18-29-30(25,26)27/h9,11,13,15,23-24H,6-8,10,12,14,16-18H2,1-5H3,(H2,25,26,27)/b20-11+,21-13+,22-15+/t23-/m0/s1

InChI Key

BJLPWUCPFAJINB-UAQSTNRTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acyclic diterpenoids. These are diterpenoids (compounds made of four consecutive isoprene units) that do not contain a cycle.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Acyclic diterpenoids

Alternative Parents

Substituents

Acyclic diterpenoid
1-(1z-alkenyl)-glycero-3-phosphate
Monoalkylglycerophosphate
Sn-glycerol-3-phosphate
Glycerophospholipid
Monoalkyl phosphate
Glycerol ether
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Secondary alcohol
Ether
Dialkyl ether
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-O-(geranylgeranyl)glycerol 1-phosphate (CHEBI:16206 )
Monoalkylglycerophosphates (C04590 )
Monoalkylglycerophosphates (LMGP10060002 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00091 g/L	ALOGPS
logP	4.33	ALOGPS
logP	5.02	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Acidic)	1.51	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	96.22 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	126.67 m³·mol⁻¹	ChemAxon
Polarizability	50.81 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-2345900000-50810c2a67d5d06ad4e5	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9877200000-04610e3bf5764b71fff7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0592-6593000000-292bf8b547ed889165ce	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002f-6120900000-e79a55dafe66d5c8e696	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-2f7c8908c9c3a0a45af4	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b87a07aa7166af9bd570	2019-02-23	View Spectrum

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

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
Archaea/Archaea	Euryarchaeota	37
Archaea/Archaea	Crenarchaeota	20
Archaea/Archaea	Korarchaeota	1
Archaea	Euryarchaeota	2
Archaea	Crenarchaeota	1
Archaea/Archaea	Thaumarchaeota	2
Bacteria	Bacteroidetes	4	Human feces

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

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

C04590

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11705814

PDB ID

Not Available

ChEBI ID

16206

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 sn-3-O-(geranylgeranyl)glycerol 1-phosphate (MMDBc0054664)

MOL for #<Metabolite:0x00007fece8c46468>

3D MOL for #<Metabolite:0x00007fece8c46468>

3D SDF for #<Metabolite:0x00007fece8c46468>

3D-SDF for #<Metabolite:0x00007fece8c46468>

PDB for #<Metabolite:0x00007fece8c46468>

3D PDB for #<Metabolite:0x00007fece8c46468>

SMILES for #<Metabolite:0x00007fece8c46468>

INCHI for #<Metabolite:0x00007fece8c46468>

Structure for #<Metabolite:0x00007fece8c46468>

3D Structure for #<Metabolite:0x00007fece8c46468>