4ALU

Benzofuropyrimidinone Inhibitors of Pim-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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, 4ALW

  • 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 limitation ...

    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)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
79O (Subject of Investigation/LOI)
Query on 79O

Download Ideal Coordinates CCD File 
C [auth A]8-bromo-2-(2-chlorophenyl)[1]benzofuro[3,2-d]pyrimidin-4(3H)-one
C16 H8 Br Cl N2 O2
UGRPNQCFWPYERM-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
79O PDBBind:  4ALU IC50: 17 (nM) from 1 assay(s)
BindingDB:  4ALU IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.162α = 90
b = 97.162β = 90
c = 81.053γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Data collection