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 
  • R-Value Observed: 0.214 

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
  • Primary Citation of Related Structures:  
    3ZIM

  • 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 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 ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORMA940Homo sapiensMutation(s): 0 
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
PHAROS:  P42336
GTEx:  ENSG00000121879
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KKR
Query on KKR
Download Ideal Coordinates CCD File 
 B [auth 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
C30 H35 N7 O3 S
DLNUPKDFXMWRFP-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KKRIC50:  6.800000190734863   nM  BindingDB
KKREC50:  10   nM  BindingDB
KKRIC50 :  6.800000190734863   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 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.34α = 90
b = 135.027β = 90
c = 142.921γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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