7TZ7

PI3K alpha in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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, Emeryville, California 94608, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform1,074Homo sapiensMutation(s): 2 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Phosphatidylinositol 3-kinase regulatory subunit alpha291Homo sapiensMutation(s): 0 
Gene Names: PIK3R1GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KVJ (Subject of Investigation/LOI)
Query on KVJ

Download Ideal Coordinates CCD File 
C [auth A](4S,5R)-3-[2'-amino-2-(morpholin-4-yl)-4'-(trifluoromethyl)[4,5'-bipyrimidin]-6-yl]-4-(hydroxymethyl)-5-methyl-1,3-oxazolidin-2-one
C18 H20 F3 N7 O4
IEYOHYVYEJVEJJ-SKDRFNHKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.87α = 90
b = 109.672β = 90
c = 135.242γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

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: 2023-10-18
    Changes: Data collection, Refinement description