7R2B | pdb_00007r2b

PI3Kdelta in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7R2B/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-02-04 Released: 2022-05-18 
• Deposition Author(s): Gutmann, S., Rummel, G., Shrestha, B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Identification of NVP-CLR457 as an Orally Bioavailable Non-CNS-Penetrant pan-Class IA Phosphoinositol-3-Kinase Inhibitor.

Fairhurst, R.A., Furet, P., Imbach-Weese, P., Stauffer, F., Rueeger, H., McCarthy, C., Ripoche, S., Oswald, S., Arnaud, B., Jary, A., Maira, M., Schnell, C., Guthy, D.A., Wartmann, M., Kiffe, M., Desrayaud, S., Blasco, F., Widmer, T., Seiler, F., Gutmann, S., Knapp, M., Caravatti, G.

(2022) J Med Chem 65: 8345-8379

• PubMed: 35500094 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c00267
• Primary Citation Related Structures: 
  7R26, 7R2B, 7TZ7


• PubMed Abstract: 
  

  Balanced pan-class I phosphoinositide 3-kinase inhibition as an approach to cancer treatment offers the prospect of treating a broad range of tumor types and/or a way to achieve greater efficacy with a single inhibitor. Taking buparlisib as the starting point, the balanced pan-class I PI3K inhibitor 40 (NVP-CLR457) was identified with what was considered to be a best-in-class profile. Key to the optimization to achieve this profile was eliminating a microtubule stabilizing off-target activity, balancing the pan-class I PI3K inhibition profile, minimizing CNS penetration, and developing an amorphous solid dispersion formulation. A rationale for the poor tolerability profile of 40 in a clinical study is discussed.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland.
Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 108.25 kDa 
• Atom Count: 5,971 
• Modeled Residue Count: 794 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	940	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H5I (Subject of Investigation/LOI)	B [auth A]	(4~{S})-3-[6-[2-azanyl-4-(trifluoromethyl)pyrimidin-5-yl]-2-morpholin-4-yl-pyrimidin-4-yl]-4-methyl-1,3-oxazolidin-2-one C17 H18 F3 N7 O3 FBOZVYXXWXOUOV-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.29	α = 90
b = 64.056	β = 103.19
c = 117.185	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Gutmann, S., Rummel, G., Shrestha, B.

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Funding Organization	Location	Grant Number
Not funded	Switzerland	--

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description