5KAE | pdb_00005kae

Crystal structure of human PI3K-gamma in complex with quinoline-containing inhibitor 5g

• PDB DOI: https://doi.org/10.2210/pdb5KAE/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2017-06-21 
• Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Discovery and in vivo evaluation of the potent and selective PI3K-delta inhibitors AM-0687 and AM-1430

Gonzalez-Lopez de Turiso, F., Hao, X., Shin, Y., Bui, M., Campuzano, I., Cardozo, M., Dunn, M.C., Duquette, J., Fisher, B., Foti, R.S., Henne, K., He, X., Hu, Y.-L., Kelly, R.C., Johnson, M.G., Lucas, B.S., McCarter, J., McGee, L.R., Medina, J.C., Metz, D., San Miguel, T., Mohn, D., Tran, T., Vissinga, C., Wannberg, S., Whittington, D.A., Whoriskey, J., Yu, G., Zalameda, L., Zhang, X., Cushing, T.D.

To be published.

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: 110.55 kDa 
• Atom Count: 6,908 
• Modeled Residue Count: 840 
• Deposited Residue Count: 959 
• 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	959	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RF	E [auth A]	4-azanyl-6-[[(1~{S})-1-(6-fluoranyl-3-phenyl-4-piperazin-1-ylcarbonyl-quinolin-2-yl)ethyl]amino]pyrimidine-5-carbonitrile C27 H25 F N8 O QPRMAEKTXODJGJ-INIZCTEOSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.578	α = 90
b = 67.661	β = 95.05
c = 106.197	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description