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Identification
NameGeranyl Diphosphate
Accession NumberDB02552  (EXPT01640)
TypeSmall Molecule
GroupsExperimental
DescriptionNot Available
Structure
Thumb
SynonymsNot Available
External Identifiers Not Available
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International BrandsNot Available
Brand mixturesNot Available
SaltsNot Available
Categories
UNIINot Available
CAS numberNot Available
WeightAverage: 314.2091
Monoisotopic: 314.068426018
Chemical FormulaC10H20O7P2
InChI KeyGVVPGTZRZFNKDS-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[P@@](=O)(O)OP(=O)(O)O
Pharmacology
IndicationNot Available
Structured Indications Not Available
PharmacodynamicsNot Available
Mechanism of action
TargetKindPharmacological actionActionsOrganismUniProt ID
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseProteinunknownNot AvailableShigella flexneriP62619 details
Bifunctional enzyme IspD/IspFProteinunknownNot AvailableCampylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)Q9PM68 details
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseProteinunknownNot AvailableEscherichia coli (strain K12)P62617 details
Farnesyl pyrophosphate synthaseProteinunknownNot AvailableHumanP14324 details
PrenyltransferaseProteinunknownNot AvailableStreptomyces sp. (strain CL190)Q4R2T2 details
Geranylgeranyl pyrophosphate synthaseProteinunknownNot AvailableHumanO95749 details
(2Z,6E)-farnesyl diphosphate synthaseProteinunknownNot AvailableMycobacterium tuberculosisO53434 details
Decaprenyl diphosphate synthaseProteinunknownNot AvailableMycobacterium tuberculosisP60479 details
Related Articles
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
Pathways
PathwayCategorySMPDB ID
Alendronate Action PathwayDrug actionSMP00095
Zoledronate Action PathwayDrug actionSMP00107
Wolman diseaseDiseaseSMP00511
Pravastatin Action PathwayDrug actionSMP00089
Risedronate Action PathwayDrug actionSMP00112
HypercholesterolemiaDiseaseSMP00209
Rosuvastatin Action PathwayDrug actionSMP00092
Fluvastatin Action PathwayDrug actionSMP00119
CHILD SyndromeDiseaseSMP00387
Hyper-IgD syndromeDiseaseSMP00509
Cerivastatin Action PathwayDrug actionSMP00111
Pamidronate Action PathwayDrug actionSMP00117
Atorvastatin Action PathwayDrug actionSMP00131
Cholesteryl ester storage diseaseDiseaseSMP00508
Mevalonic aciduriaDiseaseSMP00510
Steroid BiosynthesisMetabolicSMP00023
Ibandronate Action PathwayDrug actionSMP00079
Simvastatin Action PathwayDrug actionSMP00082
Lovastatin Action PathwayDrug actionSMP00099
Lysosomal Acid Lipase Deficiency (Wolman Disease)DiseaseSMP00319
DesmosterolosisDiseaseSMP00386
Chondrodysplasia Punctata II, X Linked Dominant (CDPX2)DiseaseSMP00388
Smith-Lemli-Opitz Syndrome (SLOS)DiseaseSMP00389
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available
References
Synthesis Reference

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

US20130011888
General ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
ADMET
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 )
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental PropertiesNot 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 RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-1953000000-e5ee3340554c9ecac23eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-5910000000-82bcd2195a53b847981cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gc0-9400000000-f87d391f1b3c01743515View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0509000000-43083a162145718cd977View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9500000000-053b6323e620a16328a8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-4faed4c921d605619cafView in MoNA
Taxonomy
DescriptionThis 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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassIsoprenoid phosphates
Direct ParentIsoprenoid phosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Monoterpenoid
  • Isoprenoid phosphate
  • Acyclic monoterpenoid
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors

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-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).
Gene Name:
ispF
Uniprot ID:
P62619
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-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) (IspF).
Gene Name:
ispDF
Uniprot ID:
Q9PM68
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:
Zinc 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-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-diphosphocytid...
Gene Name:
ispF
Uniprot ID:
P62617
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, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, d...
Gene Name:
FDPS
Uniprot ID:
P14324
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
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
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:
Lipid transport and metabolism
Specific Function:
Generates Z-farnesyl diphosphate (Z-FPP) from isopentenyl pyrophosphate (IPP). Z-FPP is the precursor of decaprenyl diphosphate, which has a central role in the biosynthesis of the mycobacterial cell wall
Gene Name:
Rv1086
Uniprot ID:
O53434
Molecular Weight:
29410.0 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:
Not Available
Specific Function:
Not Available
Gene Name:
uppS
Uniprot ID:
P60479
Molecular Weight:
Not Available
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 ]
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Drug created on June 13, 2005 07:24 / Updated on August 17, 2016 12:23