8G9C image
Entry Detail
PDB ID:
8G9C
Keywords:
Title:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- difluoromethylenebisphosphonate inositol pentakisphosphate (5-PCF2P-IP5), an analogue of 5-InsP7
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-02-21
Release Date:
2024-01-03
Method Details:
Experimental Method:
Resolution:
1.40 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Diphosphoinositol polyphosphate phosphohydrolase 1
Chain IDs:A
Chain Length:172
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs.
Chemistry 29 e202302426 e202302426 (2023)
PMID: 37773020 DOI: 10.1002/chem.202302426

Abstact

Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.

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