4GB9

Potent and Highly Selective Benzimidazole Inhibitors of PI3K-delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.438 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent and highly selective benzimidazole inhibitors of PI3-kinase delta.

Murray, J.M.Sweeney, Z.K.Chan, B.K.Balazs, M.Bradley, E.Castanedo, G.Chabot, C.Chantry, D.Flagella, M.Goldstein, D.M.Kondru, R.Lesnick, J.Li, J.Lucas, M.C.Nonomiya, J.Pang, J.Price, S.Salphati, L.Safina, B.Savy, P.P.Seward, E.M.Ultsch, M.Sutherlin, D.P.

(2012) J.Med.Chem. 55: 7686-7695

  • DOI: 10.1021/jm300717c

  • PubMed Abstract: 
  • Inhibition of PI3Kδ is considered to be an attractive mechanism for the treatment of inflammatory diseases and leukocyte malignancies. Using a structure-based design approach, we have identified a series of potent and selective benzimidazole-based in ...

    Inhibition of PI3Kδ is considered to be an attractive mechanism for the treatment of inflammatory diseases and leukocyte malignancies. Using a structure-based design approach, we have identified a series of potent and selective benzimidazole-based inhibitors of PI3Kδ. These inhibitors do not occupy the selectivity pocket between Trp760 and Met752 that is induced by other families of PI3Kδ inhibitors. Instead, the selectivity of the compounds for inhibition of PI3Kδ relative to other PI3K isoforms appears to be due primarily to the strong interactions these inhibitors are able to make with Trp760 in the PI3Kδ binding pocket. The pharmacokinetic properties and the ability of compound 5 to inhibit the function of B-cells in vivo are described.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. murray.jeremy@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
966Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153
Find proteins for P48736 (Homo sapiens)
Go to Gene View: PIK3CG
Go to UniProtKB:  P48736
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0WR
Query on 0WR

Download SDF File 
Download CCD File 
A
2-[1-({2-[2-(dimethylamino)-1H-benzimidazol-1-yl]-9-methyl-6-(morpholin-4-yl)-9H-purin-8-yl}methyl)piperidin-4-yl]propan-2-ol
C28 H39 N9 O2
SUPBDTZKRDSWGT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0WRIC50: 540 nM (100) BINDINGDB
0WRIC50: 540 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.438 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.350α = 90.00
b = 66.020β = 98.00
c = 102.280γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
DENZOdata reduction
XSCALEdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-07-26 
  • Released Date: 2012-08-22 
  • Deposition Author(s): Murray, J.M.

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references