Identification
- Generic Name
- Geranyl Diphosphate
- DrugBank Accession Number
- DB02552
- Background
Not Available
- Type
- Small Molecule
- Groups
- Experimental
- Structure
Structure for Geranyl Diphosphate (DB02552)
- Weight
- Average: 314.2091
Monoisotopic: 314.068426018 - Chemical Formula
- C10H20O7P2
- Synonyms
- Not Available
Pharmacology
- Indication
Not Available
Reduce drug development failure ratesBuild, train, & validate machine-learning modelswith evidence-based and structured datasets.Build, train, & validate predictive machine-learning models with structured datasets.- Contraindications & Blackbox Warnings
Prevent Adverse Drug Events TodayTap into our Clinical API for life-saving information on contraindications & blackbox warnings, population restrictions, harmful risks, & more.Avoid life-threatening adverse drug events with our Clinical API- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Not Available Escherichia coli (strain K12) UFarnesyl pyrophosphate synthase Not Available Humans UPrenyltransferase Not Available Streptomyces sp. (strain CL190) UGeranylgeranyl pyrophosphate synthase Not Available Humans U(2Z,6E)-farnesyl diphosphate synthase Not Available Mycobacterium tuberculosis UDecaprenyl diphosphate synthase Not Available Mycobacterium tuberculosis U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Not Available Shigella flexneri UBifunctional enzyme IspD/IspF Not Available Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) - 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
- Adverse Effects
Improve decision support & research outcomesWith structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!Improve decision support & research outcomes with our structured adverse effects data.- Toxicity
Not Available
- Pathways
Pathway Category Lovastatin Action Pathway Drug action Cerivastatin Action Pathway Drug action Hypercholesterolemia Disease Chondrodysplasia Punctata II, X-Linked Dominant (CDPX2) Disease Smith-Lemli-Opitz Syndrome (SLOS) Disease Mevalonic Aciduria Disease Simvastatin Action Pathway Drug action Pravastatin Action Pathway Drug action Rosuvastatin Action Pathway Drug action Zoledronate Action Pathway Drug action Pamidronate Action Pathway Drug action Fluvastatin Action Pathway Drug action Lysosomal Acid Lipase Deficiency (Wolman Disease) Disease Cholesteryl Ester Storage Disease Disease Steroid Biosynthesis Metabolic Ibandronate Action Pathway Drug action Alendronate Action Pathway Drug action Risedronate Action Pathway Drug action Atorvastatin Action Pathway Drug action Desmosterolosis Disease CHILD Syndrome Disease Hyper-IgD Syndrome Disease Wolman Disease Disease - Pharmacogenomic Effects/ADRs
- Not Available
Interactions
- Drug Interactions
- This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Drug Interaction Integrate drug-drug
interactions in your softwareAluminum hydroxide Aluminum hydroxide can cause a decrease in the absorption of Geranyl Diphosphate resulting in a reduced serum concentration and potentially a decrease in efficacy. Calcium acetate Calcium acetate can cause a decrease in the absorption of Geranyl Diphosphate resulting in a reduced serum concentration and potentially a decrease in efficacy. Calcium carbonate Calcium carbonate can cause a decrease in the absorption of Geranyl Diphosphate resulting in a reduced serum concentration and potentially a decrease in efficacy. Calcium chloride Calcium chloride can cause a decrease in the absorption of Geranyl Diphosphate resulting in a reduced serum concentration and potentially a decrease in efficacy. Calcium citrate Calcium citrate can cause a decrease in the absorption of Geranyl Diphosphate resulting in a reduced serum concentration and potentially a decrease in efficacy. - Food Interactions
- Not Available
Categories
- Drug Categories
- Chemical TaxonomyProvided by Classyfire
- 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
- Acyclic monoterpenoid / Aliphatic acyclic compound / Alkyl phosphate / Hydrocarbon derivative / Isoprenoid phosphate / Monoalkyl phosphate / Monoterpenoid / Organic oxide / Organic oxygen compound / Organic phosphoric acid derivative
- Molecular Framework
- Aliphatic acyclic compounds
- External Descriptors
- polyprenol diphosphate (CHEBI:17211) / Acyclic monoterpenoids, Linear monoterpenes (C00341) / Acyclic monoterpenoids (LMPR0102010001)
- Affected organisms
- Not Available
Chemical Identifiers
- UNII
- 7X7DBM66JG
- CAS number
- Not Available
- 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[P@@](=O)(O)OP(=O)(O)O
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
- HMDB0001285
- KEGG Compound
- C05847
- PubChem Compound
- 445995
- PubChem Substance
- 46504900
- ChemSpider
- 393471
- ChEBI
- 17211
- ChEMBL
- CHEMBL41342
- ZINC
- ZINC000008215849
- PDBe Ligand
- GPP
- PDB Entries
- 1h47 / 1h48 / 1ubw / 1w55 / 1w57 / 1yqn / 1zcw / 2amt / 2e8x / 2gzl … show 29 more
Clinical Trials
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
Property Value Source Water Solubility 0.902 mg/mL ALOGPS logP 1.63 ALOGPS logP 1.96 Chemaxon logS -2.5 ALOGPS pKa (Strongest Acidic) 1.77 Chemaxon Physiological Charge -3 Chemaxon Hydrogen Acceptor Count 5 Chemaxon Hydrogen Donor Count 3 Chemaxon Polar Surface Area 113.29 Å2 Chemaxon Rotatable Bond Count 8 Chemaxon Refractivity 72.93 m3·mol-1 Chemaxon Polarizability 28.52 Å3 Chemaxon Number of Rings 0 Chemaxon Bioavailability 1 Chemaxon Rule of Five Yes Chemaxon Ghose Filter Yes Chemaxon Veber's Rule No Chemaxon MDDR-like Rule No Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption - 0.681 Blood Brain Barrier + 0.7921 Caco-2 permeable - 0.5967 P-glycoprotein substrate Substrate 0.5257 P-glycoprotein inhibitor I Non-inhibitor 0.8021 P-glycoprotein inhibitor II Non-inhibitor 0.6218 Renal organic cation transporter Non-inhibitor 0.9235 CYP450 2C9 substrate Non-substrate 0.8276 CYP450 2D6 substrate Non-substrate 0.828 CYP450 3A4 substrate Non-substrate 0.5088 CYP450 1A2 substrate Non-inhibitor 0.8244 CYP450 2C9 inhibitor Non-inhibitor 0.7835 CYP450 2D6 inhibitor Non-inhibitor 0.8795 CYP450 2C19 inhibitor Non-inhibitor 0.7799 CYP450 3A4 inhibitor Non-inhibitor 0.8565 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.8918 Ames test Non AMES toxic 0.7621 Carcinogenicity Non-carcinogens 0.6 Biodegradation Ready biodegradable 0.6376 Rat acute toxicity 2.4092 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.7452 hERG inhibition (predictor II) Non-inhibitor 0.8614
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
Spectrum Spectrum Type Splash Key Predicted GC-MS Spectrum - GC-MS Predicted GC-MS splash10-004j-9640000000-9ce32c835bdcfa97fa15 Predicted MS/MS Spectrum - 10V, Positive (Annotated) Predicted LC-MS/MS splash10-014i-1429000000-807db8e485235cd7b8c0 Predicted MS/MS Spectrum - 10V, Negative (Annotated) Predicted LC-MS/MS splash10-03di-0009000000-5982e234821104189fa4 Predicted MS/MS Spectrum - 20V, Positive (Annotated) Predicted LC-MS/MS splash10-000i-1910000000-a1d8cfc0cf193cbeff48 Predicted MS/MS Spectrum - 20V, Negative (Annotated) Predicted LC-MS/MS splash10-06vi-7917000000-b9f74aa29d143742cf75 Predicted MS/MS Spectrum - 40V, Negative (Annotated) Predicted LC-MS/MS splash10-004i-9000000000-f06c76fd42524853c864 Predicted MS/MS Spectrum - 40V, Positive (Annotated) Predicted LC-MS/MS splash10-067l-9400000000-5ac747793d37d72c4b14 Predicted 1H NMR Spectrum 1D NMR Not Applicable Predicted 13C NMR Spectrum 1D NMR Not Applicable - Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 185.6345328 predictedDarkChem Lite v0.1.0 [M-H]- 181.9397328 predictedDarkChem Lite v0.1.0 [M-H]- 164.37737 predictedDeepCCS 1.0 (2019) [M+H]+ 166.73537 predictedDeepCCS 1.0 (2019) [M+Na]+ 173.10919 predictedDeepCCS 1.0 (2019)
Targets
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- 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
- 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. [Article]
- Kind
- Protein
- Organism
- Humans
- 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
- 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. [Article]
- 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
- 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. [Article]
- Kind
- Protein
- Organism
- Humans
- 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
- 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. [Article]
- 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
- 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. [Article]
- 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
- 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. [Article]
- 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
- 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
- Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
- 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. [Article]
- 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. [Article]
Drug created at June 13, 2005 13:24 / Updated at August 01, 2020 13:43