MiMeDB: Showing metabocard for (2E,6E,10E)-geranylgeranyl diphosphate (MMDBc0054036)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:47:39 UTC

Update Date

2024-04-20 06:12:02 UTC

Metabolite ID

MMDBc0054036

Metabolite Identification

Common Name

(2E,6E,10E)-geranylgeranyl diphosphate

Description

all-trans-geranyl-geranyl diphosphate 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. all-trans-geranyl-geranyl diphosphate is a moderately acidic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04141515322D          

 32 31  0  0  0  0            999 V2000
   -4.8947   -4.6440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8947   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4197   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0552   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5302    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2447   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7697   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -3.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4197   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1822   -2.5006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0552   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2927   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5302   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7677    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4822   -3.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0072   -2.5006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4677   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9427    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7677    4.6440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8947    4.3420    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.4657    3.5170    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.8947    2.0881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4657    2.9131    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.7677    1.7861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5927    3.2151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    3.9295    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    2.5006    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7697   -3.2151    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052   -1.7861    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802   -0.3572    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  6  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 17  1  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  2  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 18 11  2  0  0  0  0
 19  4  1  0  0  0  0
 19 12  1  0  0  0  0
 19 13  2  0  0  0  0
 20  5  1  0  0  0  0
 20 14  1  0  0  0  0
 20 15  2  0  0  0  0
 26 16  1  0  0  0  0
 28 21  2  0  0  0  0
 28 22  1  0  0  0  0
 28 23  1  0  0  0  0
 28 27  1  0  0  0  0
 29 24  2  0  0  0  0
 29 25  1  0  0  0  0
 29 26  1  0  0  0  0
 29 27  1  0  0  0  0
 30 11  1  0  0  0  0
 31 13  1  0  0  0  0
 32 15  1  0  0  0  0
M  CHG  3  22  -1  23  -1  25  -1
M  END


  Mrv0541 04141515322D          

 32 31  0  0  0  0            999 V2000
   -4.8947   -4.6440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8947   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4197   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0552   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5302    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2447   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7697   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6572   -3.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4197   -3.2151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1822   -2.5006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0552   -1.7861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2927   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5302   -0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7677    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4822   -3.9295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0072   -2.5006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4677   -1.0717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9427    0.3572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7677    4.6440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8947    4.3420    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.4657    3.5170    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.8947    2.0881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4657    2.9131    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.7677    1.7861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5927    3.2151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    3.9295    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802    2.5006    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7697   -3.2151    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052   -1.7861    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1802   -0.3572    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  6  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 17  1  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  2  0  0  0  0
 18  3  1  0  0  0  0
 18 10  1  0  0  0  0
 18 11  2  0  0  0  0
 19  4  1  0  0  0  0
 19 12  1  0  0  0  0
 19 13  2  0  0  0  0
 20  5  1  0  0  0  0
 20 14  1  0  0  0  0
 20 15  2  0  0  0  0
 26 16  1  0  0  0  0
 28 21  2  0  0  0  0
 28 22  1  0  0  0  0
 28 23  1  0  0  0  0
 28 27  1  0  0  0  0
 29 24  2  0  0  0  0
 29 25  1  0  0  0  0
 29 26  1  0  0  0  0
 29 27  1  0  0  0  0
 30 11  1  0  0  0  0
 31 13  1  0  0  0  0
 32 15  1  0  0  0  0
M  CHG  3  22  -1  23  -1  25  -1
M  END
> <DATABASE_ID>
MMDBc0054036

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)/p-3/b18-11+,19-13+,20-15+

> <INCHI_KEY>
OINNEUNVOZHBOX-QIRCYJPOSA-K

> <FORMULA>
C20H33O7P2

> <MOLECULAR_WEIGHT>
447.426

> <EXACT_MASS>
447.171798138

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
46.196966859910845

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl (phosphonatooxy)phosphonate

> <ALOGPS_LOGP>
4.70

> <JCHEM_LOGP>
5.276447335666666

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2043406094078315

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186885241006

> <JCHEM_POLAR_SURFACE_AREA>
121.78

> <JCHEM_REFRACTIVITY>
117.16799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.58e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl phosphonatooxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-APR-15         0                                  
HETATM    1  C   UNK     0      -9.137  -8.669   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.137  -6.002   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.517  -3.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.103  -0.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.723   2.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.057  -6.002   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.437  -3.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.183  -0.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.827  -7.335   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.517  -6.002   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.207  -4.668   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.103  -3.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.413  -2.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.723  -0.667   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.033   0.667   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.803   2.001   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.367  -7.335   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.747  -4.668   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.873  -2.001   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.493   0.667   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.033   8.669   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.137   8.105   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0       6.469   6.565   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0       9.137   3.898   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       6.469   5.438   0.000  0.00  0.00           O-1
HETATM   26  O   UNK     0       7.033   3.334   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       8.573   6.002   0.000  0.00  0.00           O+0
HETATM   28  P   UNK     0       7.803   7.335   0.000  0.00  0.00           P+0
HETATM   29  P   UNK     0       7.803   4.668   0.000  0.00  0.00           P+0
HETATM   30  H   UNK     0      -1.437  -6.002   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       3.183  -3.334   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       7.803  -0.667   0.000  0.00  0.00           H+0
CONECT    1   17                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4   19                                                            
CONECT    5   20                                                            
CONECT    6    9   10                                                       
CONECT    7   11   12                                                       
CONECT    8   13   14                                                       
CONECT    9    6   17                                                       
CONECT   10    6   18                                                       
CONECT   11    7   18   30                                                  
CONECT   12    7   19                                                       
CONECT   13    8   19   31                                                  
CONECT   14    8   20                                                       
CONECT   15   16   20   32                                                  
CONECT   16   15   26                                                       
CONECT   17    1    2    9                                                  
CONECT   18    3   10   11                                                  
CONECT   19    4   12   13                                                  
CONECT   20    5   14   15                                                  
CONECT   21   28                                                            
CONECT   22   28                                                            
CONECT   23   28                                                            
CONECT   24   29                                                            
CONECT   25   29                                                            
CONECT   26   16   29                                                       
CONECT   27   28   29                                                       
CONECT   28   21   22   23   27                                             
CONECT   29   24   25   26   27                                             
CONECT   30   11                                                            
CONECT   31   13                                                            
CONECT   32   15                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   62    0
END

Synonyms

Value	Source
all-trans-Geranylgeranyl diphosphate	ChEBI
all-trans-Geranylgeranyl diphosphoric acid	Generator
all-trans-Geranyl-geranyl diphosphoric acid	Generator
2-trans,6-trans,10-trans-Geranylgeranyl diphosphoric acid(3-)	Generator
Geranylgeranyl pyrophosphate, (Z,e,e)-isomer	MeSH
Geranylgeranyl pyrophosphate, 14C-labeled, (e,e,e)-isomer	MeSH
GGPP CPD	MeSH
Geranylgeranyl pyrophosphate	MeSH
Geranylgeraniol diphosphate	MeSH
GGPP Diphosphate	MeSH
Nerylneryl diphosphate	MeSH
Geranylgeranyl diphosphate	MeSH

Molecular Formula

C₂₀H₃₃O₇P₂

Average Mass

447.426

Monoisotopic Mass

447.171798138

IUPAC Name

(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl (phosphonatooxy)phosphonate

Traditional Name

(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl phosphonatooxyphosphonate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)/p-3/b18-11+,19-13+,20-15+

InChI Key

OINNEUNVOZHBOX-QIRCYJPOSA-K

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
Organic pyrophosphate
Isoprenoid phosphate
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:58756 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.066 g/L	ALOGPS
logP	4.7	ALOGPS
logP	5.28	ChemAxon
logS	-3.9	ALOGPS
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	14	ChemAxon
Refractivity	117.17 m³·mol⁻¹	ChemAxon
Polarizability	46.2 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	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

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
Eukaryota/Fungi	Ascomycota	55	Human feces
Bacteria	Actinobacteria	10	Human
Bacteria	Proteobacteria	6	Human
Bacteria	Cyanobacteria	2
Eukaryota/Fungi	Basidiomycota	6	Human feces
Archaea/Archaea	Euryarchaeota	38
Eukaryota/Fungi	Mucoromycota	3
Archaea	Crenarchaeota	2
Archaea/Archaea	Crenarchaeota	20
Viruses/Bamfordvirae	Nucleocytoviricota	5
Archaea/Archaea	Korarchaeota	1
Archaea	Euryarchaeota	2
Archaea/Archaea	Thaumarchaeota	2
Bacteria	Bacteroidetes	4	Human feces
Bacteria	nah	2	Human
Bacteria	Chloroflexi	1

Exposure Sources

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

5497105

PDB ID

Not Available

ChEBI ID

58756

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 (2E,6E,10E)-geranylgeranyl diphosphate (MMDBc0054036)

MOL for #<Metabolite:0x00007fdb1bf3c2c8>

3D MOL for #<Metabolite:0x00007fdb1bf3c2c8>

3D SDF for #<Metabolite:0x00007fdb1bf3c2c8>

3D-SDF for #<Metabolite:0x00007fdb1bf3c2c8>

PDB for #<Metabolite:0x00007fdb1bf3c2c8>

3D PDB for #<Metabolite:0x00007fdb1bf3c2c8>

SMILES for #<Metabolite:0x00007fdb1bf3c2c8>

INCHI for #<Metabolite:0x00007fdb1bf3c2c8>

Structure for #<Metabolite:0x00007fdb1bf3c2c8>

3D Structure for #<Metabolite:0x00007fdb1bf3c2c8>