3IBE

Crystal Structure of a Pyrazolopyrimidine Inhibitor Bound to PI3 Kinase Gamma

• PDB DOI: https://doi.org/10.2210/pdb3IBE/pdb

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


• Deposited: 2009-07-15 Released: 2009-09-01 
• Deposition Author(s): Bard, J., Svenson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

ATP-Competitive Inhibitors of the Mammalian Target of Rapamycin: Design and Synthesis of Highly Potent and Selective Pyrazolopyrimidines.

Zask, A., Verheijen, J.C., Curran, K., Kaplan, J., Richard, D.J., Nowak, P., Malwitz, D.J., Brooijmans, N., Bard, J., Svenson, K., Lucas, J., Toral-Barza, L., Zhang, W.G., Hollander, I., Gibbons, J.J., Abraham, R.T., Ayral-Kaloustian, S., Mansour, T.S., Yu, K.

(2009) J Med Chem 52: 5013-5016

• PubMed: 19645448 
• DOI: https://doi.org/10.1021/jm900851f
• Primary Citation of Related Structures:  
  3IBE


• PubMed Abstract: 
  

  The mammalian target of rapamycin (mTOR), a central regulator of growth, survival, and metabolism, is a validated target for cancer therapy. Rapamycin and its analogues, allosteric inhibitors of mTOR, only partially inhibit one mTOR protein complex. ATP-competitive, global inhibitors of mTOR that have the potential for enhanced anticancer efficacy are described. Structural features leading to potency and selectivity were identified and refined leading to compounds with in vivo efficacy in tumor xenograft models.

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Organizational Affiliation: 

Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 111.46 kDa 
• Atom Count: 6,622 
• Modelled Residue Count: 850 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L64	C [auth A]	1-(4-{4-morpholin-4-yl-1-[1-(pyridin-3-ylcarbonyl)piperidin-4-yl]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}phenyl)-3-pyridin-4-ylurea C32 H32 N10 O3 HLHOHTNONYACFD-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.159	α = 90
b = 68.458	β = 94.8
c = 106.901	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Bard, J., Svenson, K.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description