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: 110.41 kDa 
• Atom Count: 6847 
• Modelled Residue Count: 841 
• Deposited Residue Count: 960 
• Unique protein chains: 1

3DBS

Structure of PI3K gamma in complex with GDC0941

• PDB DOI: 10.2210/pdb3DBS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2008-06-02 Released: 2008-06-17 
• Deposition Author(s): Wiesmann, C., Ultsch, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

The identification of 2-(1H-indazol-4-yl)-6-(4-methanesulfonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (GDC-0941) as a potent, selective, orally bioavailable inhibitor of class I PI3 kinase for the treatment of cancer

Folkes, A.J., Ahmadi, K., Alderton, W.K., Alix, S., Baker, S.J., Box, G., Chuckowree, I.S., Clarke, P.A., Depledge, P., Eccles, S.A., Friedman, L.S., Hayes, A., Hancox, T.C., Kugendradas, A., Lensun, L., Moore, P., Olivero, A.G., Pang, J., Patel, S., Pergl-Wilson, G.H., Raynaud, F.I., Robson, A., Saghir, N., Salphati, L., Sohal, S., Ultsch, M.H., Valenti, M., Wallweber, H.J.A., Wan, N.C., Wiesmann, C., Workman, P., Zhyvoloup, A., Zvelebil, M.J., Shuttleworth, S.J.

(2008) J Med Chem 51: 5522-5532

• PubMed: 18754654 
• DOI: 10.1021/jm800295d
• Primary Citation of Related Structures:  
  3DBS


• PubMed Abstract: 
  

Phosphatidylinositol-3-kinase (PI3K) is an important target in cancer due to the deregulation of the PI3K/ Akt signaling pathway in a wide variety of tumors. A series of thieno[3,2-d]pyrimidine derivatives were prepared and evaluated as inhibitors of PI3 kinase p110alpha. The synthesis, biological activity, and further profiling of these compounds are described. This work resulted in the discovery of 17, GDC-0941, which is a potent, selective, orally bioavailable inhibitor of PI3K and is currently being evaluated in human clinical trials for the treatment of cancer.

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Organizational Affiliation: 

Piramed Pharma, 957 Buckingham Avenue, Slough, Berks SL1 4NL, United Kingdom. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	960	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GD9	B [auth A]	2-(1H-indazol-4-yl)-6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-yl-thieno[3,2-d]pyrimidine C23 H27 N7 O3 S2 LHNIIDJUOCFXAP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GD9	BindingDB:  3DBS	Ki: min: 1.4, max: 41.8 (nM) from 3 assay(s)
		Kd: min: 7.7, max: 48 (nM) from 2 assay(s)
		IC50: min: 13, max: 746 (nM) from 10 assay(s)
	PDBBind:  3DBS	IC50: 75 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.284	α = 90
b = 67.762	β = 95.31
c = 106.972	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-02 
• Released Date: 2008-06-17 
Deposition Author(s): Wiesmann, C., Ultsch, M.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance