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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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Click here for structure editor
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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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

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Metabolite
IUPAC Name Click here for help
[(2E)-3,7-dimethylocta-2,6-dienyl] phosphono hydrogen phosphate
Synonyms Click here for help
geranyl pyrophosphate | GPP | neryl pyrophosphate
Database Links Click here for help
CAS Registry No. 763-10-0 (source: Scifinder)
ChEBI CHEBI:17211
ChEMBL Ligand CHEMBL41342
DrugBank Ligand DB02552
GtoPdb PubChem SID 135651490
LIPID MAPS LMPR0102010001
PubChem CID 445995
RCSB PDB Ligand GPP
Search Google for chemical match using the InChIKey GVVPGTZRZFNKDS-JXMROGBWSA-N
Search Google for chemicals with the same backbone GVVPGTZRZFNKDS
UniChem Compound Search for chemical match using the InChIKey GVVPGTZRZFNKDS-JXMROGBWSA-N
UniChem Connectivity Search for chemical match using the InChIKey GVVPGTZRZFNKDS-JXMROGBWSA-N
Wikipedia Geranyl_diphosphate