isopentenyl diphosphate   Click here for help

GtoPdb Ligand ID: 3048

Synonyms: IPP | IPPP | isopentenyl 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 6
Topological polar surface area 132.91
Molecular weight 246.01
XLogP -1.91
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(=C)CCOP(=O)(OP(=O)(O)O)O
Isomeric SMILES CC(=C)CCOP(=O)(OP(=O)(O)O)O
InChI InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
InChI Key NUHSROFQTUXZQQ-UHFFFAOYSA-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/)
References
1. Bang S, Yoo S, Yang TJ, Cho H, Hwang SW. (2011)
Isopentenyl pyrophosphate is a novel antinociceptive substance that inhibits TRPV3 and TRPA1 ion channels.
Pain, 152 (5): 1156-64. [PMID:21353389]
2. Bang S, Yoo S, Yang TJ, Cho H, Kim YG, Hwang SW. (2010)
Resolvin D1 attenuates activation of sensory transient receptor potential channels leading to multiple anti-nociception.
Br J Pharmacol, 161 (3): 707-20. [PMID:20880407]
3. Barnard GF. (1985)
Prenyltransferase from human liver.
Meth Enzymol, 110: 155-67. [PMID:4021811]
4. Barnard GF, Popják G. (1981)
Human liver prenyltransferase and its characterization.
Biochim Biophys Acta, 661 (1): 87-99. [PMID:7295734]
5. Glickman JF, Schmid A. (2007)
Farnesyl pyrophosphate synthase: real-time kinetics and inhibition by nitrogen-containing bisphosphonates in a scintillation assay.
Assay Drug Dev Technol, 5 (2): 205-14. [PMID:17477829]
6. Hahn FM, Xuan JW, Chambers AF, Poulter CD. (1996)
Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization.
Arch Biochem Biophys, 332 (1): 30-4. [PMID:8806705]
7. Hinson DD, Chambliss KL, Toth MJ, Tanaka RD, Gibson KM. (1997)
Post-translational regulation of mevalonate kinase by intermediates of the cholesterol and nonsterol isoprene biosynthetic pathways.
J Lipid Res, 38 (11): 2216-23. [PMID:9392419]
8. Kavanagh KL, Dunford JE, Bunkoczi G, Russell RG, Oppermann U. (2006)
The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding.
J Biol Chem, 281 (31): 22004-12. [PMID:16698791]
9. Matsumura Y, Kidokoro T, Miyagi Y, Marilingaiah NR, Sagami H. (2007)
The carboxyl-terminal region of the geranylgeranyl diphosphate synthase is indispensable for the stabilization of the region involved in substrate binding and catalysis.
J Biochem, 142 (4): 533-7. [PMID:17846065]
10. Runquist M, Ericsson J, Thelin A, Chojnacki T, Dallner G. (1994)
Isoprenoid biosynthesis in rat liver mitochondria. Studies on farnesyl pyrophosphate synthase and trans-prenyltransferase.
J Biol Chem, 269 (8): 5804-9. [PMID:8119922]