Geranyl Diphosphate

Identification

Name
Geranyl Diphosphate
Accession Number
DB02552  (EXPT01640)
Type
Small Molecule
Groups
Experimental
Description
Not Available
Structure
Thumb
Synonyms
Not Available
Categories
UNII
Not Available
CAS number
Not Available
Weight
Average: 314.2091
Monoisotopic: 314.068426018
Chemical Formula
C10H20O7P2
InChI Key
GVVPGTZRZFNKDS-JXMROGBWSA-N
InChI
InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
IUPAC Name
[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid
SMILES
CC(C)=CCC\C(C)=C\CO[[email protected]@](=O)(O)OP(=O)(O)O

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableShigella flexneri
UBifunctional enzyme IspD/IspFNot AvailableCampylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableEscherichia coli (strain K12)
UFarnesyl pyrophosphate synthaseNot AvailableHuman
UPrenyltransferaseNot AvailableStreptomyces sp. (strain CL190)
UGeranylgeranyl pyrophosphate synthaseNot AvailableHuman
U(2Z,6E)-farnesyl diphosphate synthaseNot AvailableMycobacterium tuberculosis
UDecaprenyl diphosphate synthaseNot AvailableMycobacterium tuberculosis
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
Not Available
Pathways
PathwayCategory
Alendronate Action PathwayDrug action
Zoledronate Action PathwayDrug action
Wolman diseaseDisease
Pravastatin Action PathwayDrug action
Risedronate Action PathwayDrug action
HypercholesterolemiaDisease
Rosuvastatin Action PathwayDrug action
Fluvastatin Action PathwayDrug action
CHILD SyndromeDisease
Hyper-IgD syndromeDisease
Cerivastatin Action PathwayDrug action
Pamidronate Action PathwayDrug action
Atorvastatin Action PathwayDrug action
Cholesteryl ester storage diseaseDisease
Mevalonic aciduriaDisease
Steroid BiosynthesisMetabolic
Ibandronate Action PathwayDrug action
Simvastatin Action PathwayDrug action
Lovastatin Action PathwayDrug action
Lysosomal Acid Lipase Deficiency (Wolman Disease)Disease
DesmosterolosisDisease
Chondrodysplasia Punctata II, X Linked Dominant (CDPX2)Disease
Smith-Lemli-Opitz Syndrome (SLOS)Disease
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

Synthesis Reference

Oscar Alvizo, Robert McDaniel, Benjamin Mijts, "PRODUCTION OF GERANYL DIPHOSPHATE." U.S. Patent US20130011888, issued January 10, 2013.

US20130011888
General References
Not Available
External Links
Human Metabolome Database
HMDB01285
KEGG Compound
C05847
PubChem Compound
445995
PubChem Substance
46504900
ChemSpider
393471
ChEBI
17211
ChEMBL
CHEMBL41342
HET
GPP
PDB Entries
1h47 / 1h48 / 1ubw / 1w55 / 1w57 / 1yqn / 1zcw / 2amt / 2e8x / 2gzl
show 18 more

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility0.902 mg/mLALOGPS
logP1.63ALOGPS
logP1.96ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity72.93 m3·mol-1ChemAxon
Polarizability28.52 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.681
Blood Brain Barrier+0.7921
Caco-2 permeable-0.5967
P-glycoprotein substrateSubstrate0.5257
P-glycoprotein inhibitor INon-inhibitor0.8021
P-glycoprotein inhibitor IINon-inhibitor0.6218
Renal organic cation transporterNon-inhibitor0.9235
CYP450 2C9 substrateNon-substrate0.8276
CYP450 2D6 substrateNon-substrate0.828
CYP450 3A4 substrateNon-substrate0.5088
CYP450 1A2 substrateNon-inhibitor0.8244
CYP450 2C9 inhibitorNon-inhibitor0.7835
CYP450 2D6 inhibitorNon-inhibitor0.8795
CYP450 2C19 inhibitorNon-inhibitor0.7799
CYP450 3A4 inhibitorNon-inhibitor0.8565
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.8918
Ames testNon AMES toxic0.7621
CarcinogenicityNon-carcinogens0.6
BiodegradationReady biodegradable0.6376
Rat acute toxicity2.4092 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.7452
hERG inhibition (predictor II)Non-inhibitor0.8614
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-00kr-1953000000-e5ee3340554c9ecac23e
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-000i-5910000000-82bcd2195a53b847981c
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0gc0-9400000000-f87d391f1b3c01743515
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-03di-0509000000-43083a162145718cd977
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9500000000-053b6323e620a16328a8
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9000000000-4faed4c921d605619caf

Taxonomy

Description
This compound 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
Organic pyrophosphates / Acyclic monoterpenoids / Monoalkyl phosphates / Organooxygen compounds / Organic oxides / Hydrocarbon derivatives
Substituents
Organic pyrophosphate / Monoterpenoid / Isoprenoid phosphate / Acyclic monoterpenoid / Monoalkyl phosphate / Alkyl phosphate / Phosphoric acid ester / Organic phosphoric acid derivative / Organic oxygen compound / Organic oxide
Molecular Framework
Aliphatic acyclic compounds
External Descriptors
polyprenol diphosphate (CHEBI:17211) / Acyclic monoterpenoids, Linear monoterpenes (C00341) / Acyclic monoterpenoids (LMPR0102010001)

Targets

Kind
Protein
Organism
Shigella flexneri
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidy...
Gene Name
ispF
Uniprot ID
P62619
Uniprot Name
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular Weight
16897.37 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423]
Kind
Protein
Organism
Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and catalyzes the conversion of 4-dipho...
Gene Name
ispDF
Uniprot ID
Q9PM68
Uniprot Name
Bifunctional enzyme IspD/IspF
Molecular Weight
41689.74 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.
Specific Function
2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase activity
Gene Name
ispF
Uniprot ID
P62617
Uniprot Name
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular Weight
16897.37 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Poly(a) rna binding
Specific Function
Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids...
Gene Name
FDPS
Uniprot ID
P14324
Uniprot Name
Farnesyl pyrophosphate synthase
Molecular Weight
48275.03 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Streptomyces sp. (strain CL190)
Pharmacological action
Unknown
General Function
Transferase activity
Specific Function
Not Available
Gene Name
Not Available
Uniprot ID
Q4R2T2
Uniprot Name
Prenyltransferase
Molecular Weight
33743.98 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.
Gene Name
GGPS1
Uniprot ID
O95749
Uniprot Name
Geranylgeranyl pyrophosphate synthase
Molecular Weight
34870.625 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Mycobacterium tuberculosis
Pharmacological action
Unknown
General Function
Catalyzes the condensation of only one isopentenyl pyrophosphate (IPP) unit in the cis configuration to E-geranyl diphosphate (E-GPP) generating the 15 carbon product (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP). Z-FPP is the precursor of decaprenyl diphosphate, which has a central role in the biosynthesis of the mycobacterial cell wall.
Specific Function
Magnesium ion binding
Gene Name
Not Available
Uniprot ID
P9WFF5
Uniprot Name
(2Z,6E)-farnesyl diphosphate synthase
Molecular Weight
29409.955 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Mycobacterium tuberculosis
Pharmacological action
Unknown
General Function
Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) in the cis configuration with (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP) generating the 50 carbon product trans,polycis-decaprenyl diphosphate. When (2E,6E)-farnesyl diphosphate (E-FPP or EE-FPP) is used in vitro, both primary products decaprenyl diphosphate and (2E,6E,10E)-geranylgeranyl diphosphate (EEE-GGPP) are synthesized. M.tuberculosis does not synthesize (2E,6E,10Z)-geranylgeranyl diphosphate (EEZ-GGPP) and heptaprenyl diphosphate. Can also accept many different allylic substrates, including E-geranyl diphosphate (E-GPP), neryl diphosphate (NPP), and all-trans-geranyl-geranyl diphosphate.
Specific Function
Di-trans,poly-cis-decaprenylcistransferase activity
Gene Name
uppS
Uniprot ID
P9WFF7
Uniprot Name
Decaprenyl diphosphate synthase
Molecular Weight
33790.985 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]

Drug created on June 13, 2005 07:24 / Updated on November 09, 2017 03:15