3ZIM

Discovery of a potent and isoform-selective targeted covalent inhibitor of the lipid kinase PI3Kalpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent and Isoform-Selective Targeted Covalent Inhibitor of the Lipid Kinase Pi3Kalpha

Nacht, M.Qiao, L.Sheets, M.P.Martin, T.S.Labenski, M.Mazdiyasni, H.Karp, R.Zhu, Z.Chaturvedi, P.Bhavsar, D.Niu, D.Westlin, W.Petter, R.C.Medikonda, A.P.Singh, J.

(2013) J.Med.Chem. 56: 712

  • DOI: 10.1021/jm3008745

  • PubMed Abstract: 
  • PI3Kα has been identified as an oncogene in human tumors. By use of rational drug design, a targeted covalent inhibitor 3 (CNX-1351) was created that potently and specifically inhibits PI3Kα. We demonstrate, using mass spectrometry and X-ray crystall ...

    PI3Kα has been identified as an oncogene in human tumors. By use of rational drug design, a targeted covalent inhibitor 3 (CNX-1351) was created that potently and specifically inhibits PI3Kα. We demonstrate, using mass spectrometry and X-ray crystallography, that the selective inhibitor covalently modifies PI3Kα on cysteine 862 (C862), an amino acid unique to the α isoform, and that PI3Kβ, -γ, and -δ are not covalently modified. 3 is able to potently (EC(50) < 100 nM) and specifically inhibit signaling in PI3Kα-dependent cancer cell lines, and this leads to a potent antiproliferative effect (GI(50) < 100 nM). A covalent probe, 8 (CNX-1220), which selectively bonds to PI3Kα, was used to investigate the duration of occupancy of 3 with PI3Kα in vivo. This is the first report of a PI3Kα-selective inhibitor, and these data demonstrate the biological impact of selectively targeting PI3Kα.


    Organizational Affiliation

    Celgene Avilomics Research, 45 Wiggins Avenue, Bedford, Massachusetts 01730, USA. mnacht@celgene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM
A
940Homo sapiensGene Names: PIK3CA
EC: 2.7.11.1, 2.7.1.153
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KKR
Query on KKR

Download SDF File 
Download CCD File 
A
1-[4-[[2-(1H-indazol-4-yl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidin-6-yl]methyl]piperazin-1-yl]-6-methyl-hept-5-ene-1,4-dione
1-[4-[[2-(1H-indazol-4-yl)-4-morpholinthieno[3,2-d]pyrimidin-6-yl]methyl]piperazin-1-yl]-6-methyl-hept-5-ene-1,4-dione
C30 H35 N7 O3 S
DLNUPKDFXMWRFP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KKRIC50: 6.8 nM (100) BINDINGDB
KKREC50: 10 nM (100) BINDINGDB
KKRIC50: 6.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.340α = 90.00
b = 135.027β = 90.00
c = 142.921γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references