5EDS

Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery, Optimization, and in Vivo Evaluation of Benzimidazole Derivatives AM-8508 and AM-9635 as Potent and Selective PI3K delta Inhibitors.

Shin, Y.Suchomel, J.Cardozo, M.Duquette, J.He, X.Henne, K.Hu, Y.L.Kelly, R.C.McCarter, J.McGee, L.R.Medina, J.C.Metz, D.San Miguel, T.Mohn, D.Tran, T.Vissinga, C.Wong, S.Wannberg, S.Whittington, D.A.Whoriskey, J.Yu, G.Zalameda, L.Zhang, X.Cushing, T.D.

(2016) J Med Chem 59: 431-447

  • DOI: 10.1021/acs.jmedchem.5b01651
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Lead optimization efforts resulted in the discovery of two potent, selective, and orally bioavailable PI3Kδ inhibitors, 1 (AM-8508) and 2 (AM-9635), with good pharmacokinetic properties. The compounds inhibit B cell receptor (BCR)-mediated AKT phosph ...

    Lead optimization efforts resulted in the discovery of two potent, selective, and orally bioavailable PI3Kδ inhibitors, 1 (AM-8508) and 2 (AM-9635), with good pharmacokinetic properties. The compounds inhibit B cell receptor (BCR)-mediated AKT phosphorylation (pAKT) in PI3Kδ-dependent in vitro cell based assays. These compounds which share a benzimidazole bicycle are effective when administered in vivo at unbound concentrations consistent with their in vitro cell potency as a consequence of improved unbound drug concentration with lower unbound clearance. Furthermore, the compounds demonstrated efficacy in a Keyhole Limpet Hemocyanin (KLH) study in rats, where the blockade of PI3Kδ activity by inhibitors 1 and 2 led to effective inhibition of antigen-specific IgG and IgM formation after immunization with KLH.


    Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
959Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P48736 (Homo sapiens)
Go to UniProtKB:  P48736
NIH Common Fund Data Resources
PHAROS  P48736
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5MT
Query on 5MT

Download CCD File 
A
4-azanyl-6-[[(1~{S})-1-[6-fluoranyl-1-(3-methylsulfonylphenyl)benzimidazol-2-yl]ethyl]amino]pyrimidine-5-carbonitrile
C21 H18 F N7 O2 S
ARGMEIUNNDIMNN-LBPRGKRZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.301α = 90
b = 68.234β = 95.12
c = 106.62γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-06
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Refinement description