(R)-5-diphosphomevalonate   Click here for help

GtoPdb Ligand ID: 3047

Synonyms: mevalonate 5-diphosphate
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 10
Hydrogen bond donors 5
Rotatable bonds 8
Topological polar surface area 190.44
Molecular weight 308.01
XLogP -3.31
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
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 OC(=O)CC(CCOP(=O)(OP(=O)(O)O)O)(O)C
Isomeric SMILES OC(=O)C[C@@](CCOP(=O)(OP(=O)(O)O)O)(O)C
InChI InChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1
InChI Key SIGQQUBJQXSAMW-ZCFIWIBFSA-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. Herdendorf TJ, Miziorko HM. (2006)
Phosphomevalonate kinase: functional investigation of the recombinant human enzyme.
Biochemistry, 45 (10): 3235-42. [PMID:16519518]
2. Herdendorf TJ, Miziorko HM. (2007)
Functional evaluation of conserved basic residues in human phosphomevalonate kinase.
Biochemistry, 46 (42): 11780-8. [PMID:17902708]
3. Michihara A, Sawamura M, Nara Y, Ikeda K, Yamori Y. (1997)
Purification and characterization of two mevalonate pyrophosphate decarboxylases from rat liver: a novel molecular species of 37 kDa.
J Biochem, 122 (3): 647-54. [PMID:9348097]
4. Qiu Y, Gao J, Guo F, Qiao Y, Li D. (2007)
Mutation and inhibition studies of mevalonate 5-diphosphate decarboxylase.
Bioorg Med Chem Lett, 17 (22): 6164-8. [PMID:17888661]
5. Qiu Y, Li D. (2006)
Inhibition of mevalonate 5-diphosphate decarboxylase by fluorinated substrate analogs.
Biochim Biophys Acta, 1760 (7): 1080-7. [PMID:16626865]
6. Toth MJ, Huwyler L, Park J. (1996)
Purification of rat liver mevalonate pyrophosphate decarboxylase.
Prep Biochem Biotechnol, 26 (1): 47-51. [PMID:8744421]
7. Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM. (2008)
Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure.
Arch Biochem Biophys, 480 (1): 58-67. [PMID:18823933]