4ALW

Benzofuropyrimidinone Inhibitors of Pim-1

• PDB DOI: https://doi.org/10.2210/pdb4ALW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


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

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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 

Starting Model: other

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

• PubMed: 22542012 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Exelixis, Department of Drug Discovery, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.07 kDa 
• Atom Count: 2,633 
• Modelled Residue Count: 273 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIM-1 KINASE	A	328	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000137193

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HY7	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
IMD	B [auth A], D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
HY7	PDBBind:  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 = 97.449	α = 90
b = 97.449	β = 90
c = 81.003	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description