trans,trans-farnesyl diphosphate   Click here for help

GtoPdb Ligand ID: 3050

Synonyms: (E,E)-farnesyl diphosphate | all-trans-farnesyl pyrophosphate | farnesyl diphosphate | FPP | trans-farnesyl pyrophosphate
PDB Ligand
Compound class: Metabolite
Click here for help

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.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 7
Hydrogen bond donors 3
Rotatable bonds 11
Topological polar surface area 132.91
Molecular weight 382.13
XLogP 1.89
No. Lipinski's rules broken 1

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
Click here for help

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/)

✖
Canonical SMILES CC(=CCOP(=O)(OP(=O)(O)O)O)CCC=C(CCC=C(C)C)C
Isomeric SMILES C/C(=C\COP(=O)(OP(=O)(O)O)O)/CC/C=C(/CCC=C(C)C)\C
InChI InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)/b14-9+,15-11+
InChI Key VWFJDQUYCIWHTN-YFVJMOTDSA-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. Fu Z, Voynova NE, Herdendorf TJ, Miziorko HM, Kim JJ. (2008)
Biochemical and structural basis for feedback inhibition of mevalonate kinase and isoprenoid metabolism.
Biochemistry, 47 (12): 3715-24. [PMID:18302342]
2. 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]
3. 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]
4. 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]
5. Shechter I, Klinger E, Rucker ML, Engstrom RG, Spirito JA, Islam MA, Boettcher BR, Weinstein DB. (1992)
Solubilization, purification, and characterization of a truncated form of rat hepatic squalene synthetase.
J Biol Chem, 267 (12): 8628-35. [PMID:1569107]
6. Tanaka RD, Schafer BL, Lee LY, Freudenberger JS, Mosley ST. (1990)
Purification and regulation of mevalonate kinase from rat liver.
J Biol Chem, 265 (4): 2391-8. [PMID:2153681]
7. Thompson JF, Danley DE, Mazzalupo S, Milos PM, Lira ME, Harwood HJ. (1998)
Truncation of human squalene synthase yields active, crystallizable protein.
Arch Biochem Biophys, 350 (2): 283-90. [PMID:9473303]
8. Voynova NE, Rios SE, Miziorko HM. (2004)
Staphylococcus aureus mevalonate kinase: isolation and characterization of an enzyme of the isoprenoid biosynthetic pathway.
J Bacteriol, 186 (1): 61-7. [PMID:14679225]