8G9E

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7

PDB DOI: https://doi.org/10.2210/pdb8G9E/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-21 Released: 2024-01-03
Deposition Author(s): Wang, H., Shears, S.B.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.175
R-Value Work: 0.124
R-Value Observed: 0.127

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs.

Hostachy, S., Wang, H., Zong, G., Franke, K., Riley, A.M., Schmieder, P., Potter, B.V.L., Shears, S.B., Fiedler, D.

(2023) Chemistry 29: e202302426-e202302426

PubMed: 37773020 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/chem.202302426
Primary Citation of Related Structures:
8G9C, 8G9D, 8G9E

PubMed Abstract:
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-IP ₅ 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-IP ₅ . 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.

Organizational Affiliation

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 38.97 kDa
Atom Count: 3,012
Modelled Residue Count: 318
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2	A	330	Homo sapiens	Mutation(s): 0 Gene Names: PPIP5K2, HISPPD1, KIAA0433, VIP2 EC: 2.7.4.21 (PDB Primary Data), 2.7.4.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43314 (Homo sapiens) Explore O43314 Go to UniProtKB: O43314
PHAROS: O43314 GTEx: ENSG00000145725
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43314
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YUT (Subject of Investigation/LOI) Query on YUT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	{difluoro[(R)-hydroxy{[(1s,2R,3S,4S,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid C₇ H₁₉ F₂ O₂₆ P₇ WXRZISRVPNTHSS-QWBQGLJISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]