Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109980.19 
• Atom Count: 7279 
• Residue Count: 940 
• Unique protein chains: 1

3ZIM

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

• DOI: 10.2210/pdb3ZIM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2013-01-09 Released: 2013-02-13 
• Deposition Author(s): 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., Jestel, A., Blaesse, M., Singh, J.

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Experimental Data Snapshot

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

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

• PubMed: 23360348 
• 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 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.

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Organizational Affiliation: 

Celgene Avilomics Research, 45 Wiggins Avenue, Bedford, Massachusetts 01730, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM	A	940	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens) Go to Gene View: PIK3CA Go to UniProtKB:  P42336

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
KKR	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
KKR	IC50: 6.8 nM (100) BINDINGDB
KKR	EC50: 10 nM (100) BINDINGDB
KKR	IC50: 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 = 59.340	α = 90.00
b = 135.027	β = 90.00
c = 142.921	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	phasing
SCALA	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-09 
• Released Date: 2013-02-13 
• Deposition Author(s): 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., Jestel, A., Blaesse, M., Singh, J.

Revision History 

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