7R26

PI3K delta in complex with SD5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SD5Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00267
  • Primary Citation of 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.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform940Mus musculusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35904
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SD5 (Subject of Investigation/LOI)
Query on SD5

Download Ideal Coordinates CCD File 
B [auth A]5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine
C18 H21 F3 N6 O2
CWHUFRVAEUJCEF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SD5 BindingDB:  7R26 Kd: 260 (nM) from 1 assay(s)
IC50: min: 110, max: 236 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.003α = 90
b = 64.53β = 103.32
c = 117.347γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SD5Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedSwitzerland--

Revision History  (Full details and data files)

  • 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