4ALV

Benzofuropyrimidinone Inhibitors of Pim-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report



Literature

The Design, Synthesis, and Biological Evaluation of Pim Kinase Inhibitors.

Tsuhako, A.L.Brown, D.S.Koltun, E.S.Aay, N.Arcalas, A.Chan, V.Du, H.Engst, S.Franzini, M.Galan, A.Huang, P.Johnston, S.Kane, B.Kim, M.H.Laird, A.D.Lin, R.Mock, L.Ngan, I.Pack, M.Stott, G.Stout, T.J.Yu, P.Zaharia, C.Zhang, W.Zhou, P.Nuss, J.M.Kearney, P.C.Xu, W.

(2012) Bioorg Med Chem Lett 22: 3732

  • DOI: 10.1016/j.bmcl.2012.04.025
  • Primary Citation of Related Structures:  
    4ALW, 4ALU, 4ALV

  • PubMed Abstract: 
  • A series of substituted benzofuropyrimidinones with pan-PIM activities and excellent selectivity against a panel of diverse kinases is described. Initial exploration identified aryl benzofuropyrimidinones that were potent, but had cell permeability l ...

    A series of substituted benzofuropyrimidinones with pan-PIM activities and excellent selectivity against a panel of diverse kinases is described. Initial exploration identified aryl benzofuropyrimidinones that were potent, but had cell permeability limitation. Using X-ray crystal structures of the bound PIM-1 complexes with 3, 5m, and 6d, we were able to guide the SAR and identify the alkyl benzofuropyrimidinone (6l) with good PIM potencies, permeability, and oral exposure.


    Organizational Affiliation

    Exelixis, Department of Drug Discovery, South San Francisco, CA 94080, USA. alew@exelixis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PIM-1A328Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R9P
Query on R9P

Download CCD File 
A
8-bromo-2-{2-chloro-4-[(piperidin-4-ylmethyl)amino]phenyl}[1]benzofuro[3,2-d]pyrimidin-4(3H)-one
C22 H20 Br Cl N4 O2
RUIXFIILMZVAAF-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R9PIC50 :  7   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.872α = 90
b = 96.872β = 90
c = 80.844γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-03-05 
  • Released Date: 2013-01-16 
  • Deposition Author(s): Stout, T.J., Adams, L.

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release