3LJ3 | pdb_00003lj3

PI3-kinase-gamma with a pyrrolopyridine-benzofuran inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LJ3/pdb

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


• Deposited: 2010-01-25 Released: 2010-04-14 
• Deposition Author(s): Bard, J., Svenson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.261 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.222 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Discovery and optimization of 2-(4-substituted-pyrrolo[2,3-b]pyridin-3-yl)methylene-4-hydroxybenzofuran-3(2H)-ones as potent and selective ATP-competitive inhibitors of the mammalian target of rapamycin (mTOR).

Tsou, H.R., MacEwan, G., Birnberg, G., Grosu, G., Bursavich, M.G., Bard, J., Brooijmans, N., Toral-Barza, L., Hollander, I., Mansour, T.S., Ayral-Kaloustian, S., Yu, K.

(2010) Bioorg Med Chem Lett 20: 2321-2325

• PubMed: 20188552 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.135
• Primary Citation Related Structures: 
  3LJ3


• PubMed Abstract: 
  

  We discovered 2-(4-substituted-pyrrolo[2,3-b]pyridin-3-yl)methylene-4-hydroxybenzofuran-3(2H)-ones as potent and selective ATP-competitive inhibitors of the mammalian target of rapamycin (mTOR). Since phenolic OH groups pose metabolic liability, one of the two hydroxyl groups was selectively removed. The SAR data showed the structural features necessary for subnanomolar inhibitory activity against mTOR kinase as well as selectivity over PI3Kalpha. An X-ray co-crystal structure of one inhibitor with the mTOR-related PI3Kgamma revealed the key hydrogen bonding interactions.

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Organizational Affiliation: 
• Chemical Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 111.35 kDa 
• Atom Count: 6,592 
• Modeled Residue Count: 829 
• 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
WYE	D [auth A]	(2Z)-4,6-dihydroxy-2-{[1-methyl-4-(4-methylpiperazin-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]methylidene}-1-benzofuran-3(2H)-one C22 H22 N4 O4 RLZIWQDVHJTWEF-NVMNQCDNSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.261 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.222 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.071	α = 90
b = 68.509	β = 94.64
c = 106.692	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Bard, J., Svenson, K.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description