3TJP | pdb_00003tjp

Crystal Structure of PI3K gamma with N6-(3,4-dimethoxyphenyl)-2-morpholino-[4,5'-bipyrimidine]-2',6-diamine

• PDB DOI: https://doi.org/10.2210/pdb3TJP/pdb

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


• Deposited: 2011-08-24 Released: 2012-08-29 
• Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

The Identification of 5-(2,4-dimorpholinopyrimidin-6-yl)-4-(trifluoromethyl)pyridin-2-amine (NVP-BKM120) as a Potent, Selective and Orally Bioavailable Class I PI3 Kinase Inhibitor for the Treatment of Cancer

Burger, M.T., Pecchi, S., Wagman, A., Ni, Z.-J., Knapp, M.S., Hendrickson, T., Atallah, G., Pfister, K., Yanchen, Z., Bartulis, S., Frazier, K., Ng, S., Smith, A., Verhagen, J., Haznedar, J., Huh, K., Iwanowicz, E., Xin, X., Menezes, D., Merritt, H., Lee, I., Weisman, M., Kaufman, S., Crawford, K., Chin, M., Bussiere, D., Shoemaker, K., Zaror, I., Maira, M., Voliva, C.

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: 111.26 kDa 
• Atom Count: 6,608 
• Modeled Residue Count: 840 
• 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): 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
13K	B [auth A]	N~6~-(3,4-dimethoxyphenyl)-2-(morpholin-4-yl)-4,5'-bipyrimidine-2',6-diamine C20 H23 N7 O3 AAKJGXGPYVKGQA-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.145	α = 90
b = 67.395	β = 96.49
c = 106.18	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description