4ALW

Benzofuropyrimidinone Inhibitors of Pim-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PIM-1 KINASE
A
328Homo sapiensGene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HY7
Query on HY7

Download SDF File 
Download CCD File 
A
8-BROMANYL-2-[(4-METHYLPIPERAZIN-1-YL)METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE
C16 H17 Br N4 O2
OOINHKLROPYETD-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HY7IC50: 27 nM (99) BINDINGDB
HY7IC50: 27 nM BINDINGMOAD
HY7IC50: 27 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.155 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.449α = 90.00
b = 97.449β = 90.00
c = 81.003γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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