MiMeDB: Showing metabocard for (E)-2-methylgeranyl diphosphate (MMDBc0055010)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:39:48 UTC

Update Date

2025-10-07 16:08:51 UTC

Metabolite ID

MMDBc0055010

Metabolite Identification

Common Name

(E)-2-methylgeranyl diphosphate

Description

(E)-2-methylgeranyl diphosphate is a terpenoid metabolite that belongs to the class of diphosphate esters. Its chemical structure features a geranyl backbone with a methyl group at the C-2 position, which distinguishes it from other geranyl derivatives. This compound is synthesized through the action of a C-methyltransferase enzyme, as evidenced by the incubation of recombinant SCO7701 protein with geranyl diphosphate and S-adenosylmethionine, resulting in the formation of (E)-2-methylgeranyl diphosphate (PMID:18563898 ). In terms of biochemical pathways, (E)-2-methylgeranyl diphosphate is involved in the biosynthesis of various terpenoids, which are essential for the production of a wide range of natural products, including essential oils and plant hormones. The modification of geranyl diphosphate to form (E)-2-methylgeranyl diphosphate highlights the intricate enzymatic processes that contribute to the diversity of terpenoid compounds in nature.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221392D          

 20 19  0  0  0  0            999 V2000
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    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
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    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
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.2868    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1270   -3.9849    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.3020   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.7309    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5559    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
   -0.8250   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.5724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
  9  6  2  0  0  0  0
 10  3  1  0  0  0  0
 10  7  1  0  0  0  0
 11  4  1  0  0  0  0
 11  8  1  0  0  0  0
 11 10  2  0  0  0  0
 17  8  1  0  0  0  0
 19 12  1  0  0  0  0
 19 13  1  0  0  0  0
 19 14  2  0  0  0  0
 19 18  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  2  0  0  0  0
 20 17  1  0  0  0  0
 20 18  1  0  0  0  0
M  CHG  3  12  -1  13  -1  15  -1
M  END
> <DATABASE_ID>
MMDBc0055010

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C)=CCC\C(C)=C(/C)COP([O-])(=O)OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H22O7P2/c1-9(2)6-5-7-10(3)11(4)8-17-20(15,16)18-19(12,13)14/h6H,5,7-8H2,1-4H3,(H,15,16)(H2,12,13,14)/p-3/b11-10+

> <INCHI_KEY>
PRUWPPRJQIGKNB-ZHACJKMWSA-K

> <FORMULA>
C11H19O7P2

> <MOLECULAR_WEIGHT>
325.215

> <EXACT_MASS>
325.062247688

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
29.740279077891053

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E)-2,3,7-trimethylocta-2,6-dien-1-yl (phosphonooxy)phosphonate

> <JCHEM_LOGP>
2.200380057333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2033041036594647

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7664606581562703

> <JCHEM_POLAR_SURFACE_AREA>
121.78

> <JCHEM_REFRACTIVITY>
73.84480000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-2,3,7-trimethylocta-2,6-dien-1-yl phosphonooxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.160   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.540   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  O   UNK     0       0.000  -8.002   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      -2.104  -7.438   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       0.564  -5.898   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.104  -3.231   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0       0.564  -4.771   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.540  -5.335   0.000  0.00  0.00           O+0
HETATM   19  P   UNK     0      -0.770  -6.668   0.000  0.00  0.00           P+0
HETATM   20  P   UNK     0      -0.770  -4.001   0.000  0.00  0.00           P+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   11                                                            
CONECT    5    6    7                                                       
CONECT    6    5    9                                                       
CONECT    7    5   10                                                       
CONECT    8   11   17                                                       
CONECT    9    1    2    6                                                  
CONECT   10    3    7   11                                                  
CONECT   11    4    8   10                                                  
CONECT   12   19                                                            
CONECT   13   19                                                            
CONECT   14   19                                                            
CONECT   15   20                                                            
CONECT   16   20                                                            
CONECT   17    8   20                                                       
CONECT   18   19   20                                                       
CONECT   19   12   13   14   18                                             
CONECT   20   15   16   17   18                                             
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

Synonyms

Value	Source
(e)-2-Methylgeranyl diphosphate	ChEBI
(e)-2-Methylgeranyl diphosphate trianion	ChEBI
(e)-2-Methylgeranyl pyrophosphate	ChEBI
(e)-2-Methylgeranyl pyrophosphate trianion	ChEBI
(e)-2-Methylgeranyl pyrophosphate(3-)	ChEBI
(e)-2-Methylgeranyl diphosphoric acid	Generator
(e)-2-Methylgeranyl diphosphoric acid trianion	Generator
(e)-2-Methylgeranyl pyrophosphoric acid	Generator
(e)-2-Methylgeranyl pyrophosphoric acid trianion	Generator
(e)-2-Methylgeranyl pyrophosphoric acid(3-)	Generator
(e)-2-Methylgeranyl diphosphoric acid(3-)	Generator

Molecular Formula

C₁₁H₁₉O₇P₂

Average Mass

325.215

Monoisotopic Mass

325.062247688

IUPAC Name

(2E)-2,3,7-trimethylocta-2,6-dien-1-yl (phosphonooxy)phosphonate

Traditional Name

(2E)-2,3,7-trimethylocta-2,6-dien-1-yl phosphonooxyphosphonate

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C(/C)COP([O-])(=O)OP([O-])([O-])=O

InChI Identifier

InChI=1S/C11H22O7P2/c1-9(2)6-5-7-10(3)11(4)8-17-20(15,16)18-19(12,13)14/h6H,5,7-8H2,1-4H3,(H,15,16)(H2,12,13,14)/p-3/b11-10+

InChI Key

PRUWPPRJQIGKNB-ZHACJKMWSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Isoprenoid phosphates

Direct Parent

Isoprenoid phosphates

Alternative Parents

Substituents

Organic pyrophosphate
Monoterpenoid
Isoprenoid phosphate
Acyclic monoterpenoid
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:61984 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	2.2	ChemAxon
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	121.78 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	73.84 m³·mol⁻¹	ChemAxon
Polarizability	29.74 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	275.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-24	25.1
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	681.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	1092.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	827.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	602.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	3005.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	110.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	427.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	657.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	518.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	344.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	215.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	9.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	381.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	126.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	451.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1459.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	1526.8

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/Eubacteria	Actinobacteria	3
Bacteria	Actinobacteria	2

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

26332462

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

51351721

PDB ID

Not Available

ChEBI ID

61984

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 (E)-2-methylgeranyl diphosphate (MMDBc0055010)

MOL for #<Metabolite:0x0000561535da4828>

3D MOL for #<Metabolite:0x0000561535da4828>

3D SDF for #<Metabolite:0x0000561535da4828>

3D-SDF for #<Metabolite:0x0000561535da4828>

PDB for #<Metabolite:0x0000561535da4828>

3D PDB for #<Metabolite:0x0000561535da4828>

SMILES for #<Metabolite:0x0000561535da4828>

INCHI for #<Metabolite:0x0000561535da4828>

Structure for #<Metabolite:0x0000561535da4828>

3D Structure for #<Metabolite:0x0000561535da4828>