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 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


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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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PIM-1 KINASEA328Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HY7
Query on HY7
Download Ideal Coordinates CCD File 
C [auth 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 Ideal Coordinates CCD File 
B [auth A],
D [auth A]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HY7 PDBBind:  4ALW IC50: 27 (nM) from 1 assay(s)
Binding MOAD:  4ALW IC50: 27 (nM) from 1 assay(s)
BindingDB:  4ALW IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.449α = 90
b = 97.449β = 90
c = 81.003γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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