Crystal structure of human PI3K-gamma in complex with CH5039699

Experimental Data Snapshot

  • Resolution: 2.82 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 

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This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Research Division, Chugai Pharmaceutical Co., Ltd , Kamakura, Kanagawa, Japan. ohwadajn@chugai-pharm.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform966Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BMW

Download Ideal Coordinates CCD File 
D [auth A]3-[7-(1H-benzimidazol-5-yl)-2-(morpholin-4-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]phenol
C23 H22 N6 O2
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.82 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.22α = 90
b = 67.87β = 95.38
c = 106.6γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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