geranyl diphosphate   Click here for help

GtoPdb Ligand ID: 3051

Synonyms: geranyl pyrophosphate | GPP | neryl pyrophosphate
PDB Ligand
Compound class: Metabolite
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 7
Hydrogen bond donors 3
Rotatable bonds 8
Topological polar surface area 132.91
Molecular weight 314.07
XLogP 0.07
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES CC(=CCOP(=O)(OP(=O)(O)O)O)CCC=C(C)C
Isomeric SMILES C/C(=C\COP(=O)(OP(=O)(O)O)O)/CCC=C(C)C
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+
InChI Key GVVPGTZRZFNKDS-JXMROGBWSA-N
Natural/Endogenous Targets
Target
diphosphomevalonate decarboxylase
mevalonate kinase
Enzymes Catalysing Reactions with this Compound as a Substrate or Product
Enzyme EC number Reaction Reference
farnesyl diphosphate synthase 2.5.1.1, 2.5.1.10 Dimethylallyl diphosphate + isopentenyl diphosphate = geranyl diphosphate + diphosphate

Geranyl diphosphate + isopentenyl diphosphate -> trans,trans-farnesyl diphosphate + diphosphate		 1-2,6
geranylgeranyl diphosphate synthase 2.5.1.1, 2.5.1.10 Dimethylallyl diphosphate + isopentenyl diphosphate = geranyl diphosphate + diphosphate

Geranyl diphosphate + isopentenyl diphosphate -> trans,trans-farnesyl diphosphate + diphosphate
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
mevalonate kinase Ligand is endogenous in the given species Hs Inhibitor Feedback inhibition 6.9 pKi - 3
⤷ pKi 6.9 (Ki 1.16x10-7 M) [3]
Description: recombinant enzyme expressed in E coli cells. Spectrophotometric assay
Conditions: pH 7.0, 25°C, saturating concentrations of substrates, 0.16-5mM ATP
mevalonate kinase Ligand is endogenous in the given species Rn Inhibitor Feedback inhibition 5.3 pIC50 - 4
⤷ pIC50 5.3 (IC50 5x10-6 M) [4]
Description: in vitro assay, enzyme expressed in E coli, purified
Conditions: pH 7.0-8.0, 30 ºC. Substrate concentrations: 4mM ATP, 3mM RS-mevalonate, 0.16mM NADH
diphosphomevalonate decarboxylase Ligand is endogenous in the given species Rn Inhibitor Feedback inhibition 4.2 – 5.3 pIC50 - 4-5
⤷ pIC50 4.2 – 5.3 (IC50 6.5x10-5 – 5x10-6 M) [4-5]
Description: expression of rat enzyme in E coli, purification, in vitro spectrophotometric assay
Conditions: Concentration of substrates: 0.16mM NADH, 4mM ATP, 36µM mevalonate 5-diphosphate. pH 7.5, 25 ºC
Targets where the ligand is described in the comment field
Target Comment
mevalonate kinase Mevalonate kinase activity is regulated by the downstream products farnesyl diphosphate and geranyl diphosphate as an example of feedback inhibition.