4AOF | pdb_00004aof

Selective small molecule inhibitor discovered by chemoproteomic assay platform reveals regulation of Th17 cell differentiation by PI3Kgamma

• PDB DOI: https://doi.org/10.2210/pdb4AOF/pdb

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


• Deposited: 2012-03-26 Released: 2012-05-09 
• Deposition Author(s): Bergamini, G., Bell, K., Shimamura, S., Werner, T., Cansfield, A., Muller, K., Perrin, J., Rau, C., Ellard, K., Hopf, C., Doce, C., Leggate, D., Mangano, R., Mathieson, T., OMahony, A., Plavec, I., Rharbaoui, F., Reinhard, F., Savitski, M.M., Ramsden, N., Hirsch, E., Drewes, G., Rausch, O., Bantscheff, M., Neubauer, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.346 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

A Selective Inhibitor Reveals Pi3Kgamma Dependence of T(H)17 Cell Differentiation.

Bergamini, G., Bell, K., Shimamura, S., Werner, T., Cansfield, A., Muller, K., Perrin, J., Rau, C., Ellard, K., Hopf, C., Doce, C., Leggate, D., Mangano, R., Mathieson, T., O'Mahony, A., Plavec, I., Rharbaoui, F., Reinhard, F., Savitski, M.M., Ramsden, N., Hirsch, E., Drewes, G., Rausch, O., Bantscheff, M., Neubauer, G.

(2012) Nat Chem Biol 8: 576

• PubMed: 22544264 
• DOI: https://doi.org/10.1038/nchembio.957
• Primary Citation Related Structures: 
  4AOF


• PubMed Abstract: 
  

  We devised a high-throughput chemoproteomics method that enabled multiplexed screening of 16,000 compounds against native protein and lipid kinases in cell extracts. Optimization of one chemical series resulted in CZC24832, which is to our knowledge the first selective inhibitor of phosphoinositide 3-kinase γ (PI3Kγ) with efficacy in in vitro and in vivo models of inflammation. Extensive target- and cell-based profiling of CZC24832 revealed regulation of interleukin-17-producing T helper cell (T(H)17) differentiation by PI3Kγ, thus reinforcing selective inhibition of PI3Kγ as a potential treatment for inflammatory and autoimmune diseases.

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Organizational Affiliation: 
• Cellzome AG, Heidelberg, Germany.

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: 110.23 kDa 
• Atom Count: 6,793 
• Modeled Residue Count: 837 
• Deposited Residue Count: 960 
• 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	960	Homo sapiens	Mutation(s): 0  EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (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
7L0	B [auth A]	N-[6-(5-methylsulfonylpyridin-3-yl)-[1,2,4]triazolo[1,5-a]pyridin-2-yl]ethanamide C14 H13 N5 O3 S RCRCKEODQLBHAY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.346 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.771	α = 90
b = 68.047	β = 94.61
c = 109.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Bergamini, G., Bell, K., Shimamura, S., Werner, T., Cansfield, A., Muller, K., Perrin, J., Rau, C., Ellard, K., Hopf, C., Doce, C., Leggate, D., Mangano, R., Mathieson, T., OMahony, A., Plavec, I., Rharbaoui, F., Reinhard, F., Savitski, M.M., Ramsden, N., Hirsch, E., Drewes, G., Rausch, O., Bantscheff, M., Neubauer, G.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Other
• Version 1.2: 2012-07-11
  Changes: Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description