3APD

Crystal structure of human PI3K-gamma in complex with CH5108134

• PDB DOI: https://doi.org/10.2210/pdb3APD/pdb

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


• Deposited: 2010-10-14 Released: 2011-04-13 
• Deposition Author(s): Nakamura, M., Fukami, T.A., Miyazaki, T., Yoshida, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.316 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Discovery and biological activity of a novel class I PI3K inhibitor, CH5132799

Ohwada, J., Ebiike, H., Kawada, H., Tsukazaki, M., Nakamura, M., Miyazaki, T., Morikami, K., Yoshinari, K., Yoshida, M., Kondoh, O., Kuramoto, S., Ogawa, K., Aoki, Y., Shimma, N.

(2011) Bioorg Med Chem Lett 21: 1767-1772

• PubMed: 21316229 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.065
• Primary Citation of Related Structures:  
  3APC, 3APD, 3APF


• PubMed Abstract: 
  

  Phosphatidylinositol 3-kinase (PI3K) is a lipid kinase and a promising therapeutic target for cancer. Using structure-based drug design (SBDD), we have identified novel PI3K inhibitors with a dihydropyrrolopyrimidine skeleton. Metabolic stability of the first lead series was drastically improved by replacing phenol with aminopyrimidine moiety. CH5132799, a novel class I PI3K inhibitor, exhibited a strong inhibitory activity especially against PI3Kα (IC(50)=0.014 μM). In human tumor cell lines with PI3K pathway activation, CH5132799 showed potent antiproliferative activity. CH5132799 is orally available and showed significant antitumor activity in PI3K pathway-activated human cancer xenograft models in mice.

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Organizational Affiliation: 

Research Division, Chugai Pharmaceutical Co., Ltd , Kamakura, Kanagawa, Japan. [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: 111.02 kDa 
• Atom Count: 6,615 
• Modelled Residue Count: 839 
• 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
MMY	B [auth A]	5-(2-Morpholin-4-yl-7-pyridin-3-yl-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl)-pyrimidin-2-ylamine C19 H20 N8 O WZVLQVVHYKFKAZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.316 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.95	α = 90
b = 67.46	β = 95.68
c = 106.28	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Nakamura, M., Fukami, T.A., Miyazaki, T., Yoshida, M.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description