Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 109.98 kDa 
• Atom Count: 7286 
• Modelled Residue Count: 886 
• Deposited Residue Count: 940 
• Unique protein chains: 1

3ZIM

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

• PDB DOI: 10.2210/pdb3ZIM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• 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 
• R-Value Observed: 0.214 

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
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
KKR	PDBBind:  3ZIM	IC50: 6.8 (nM) from 1 assay(s)
	BindingDB:  3ZIM	IC50: 6.8 (nM) from 1 assay(s)
		EC50: 10 (nM) from 1 assay(s)

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 = 59.34	α = 90
b = 135.027	β = 90
c = 142.921	γ = 90

Software Package:

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

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
  Changes: Database references