4GB9

Potent and Highly Selective Benzimidazole Inhibitors of PI3K-delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm300717c
  • Primary Citation of Related Structures:  
    4GB9

  • 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 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:  (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
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0WR
Query on 0WR

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0WR PDBBind:  4GB9 IC50: 540 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.35α = 90
b = 66.02β = 98
c = 102.28γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description