3R00

The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors.

Xiang, Y.Hirth, B.Asmussen, G.Biemann, H.P.Bishop, K.A.Good, A.Fitzgerald, M.Gladysheva, T.Jain, A.Jancsics, K.Liu, J.Metz, M.Papoulis, A.Skerlj, R.Stepp, J.D.Wei, R.R.

(2011) Bioorg Med Chem Lett 21: 3050-3056

  • DOI: 10.1016/j.bmcl.2011.03.030
  • Primary Citation of Related Structures:  
    3R00, 3R01, 3R02, 3R04

  • PubMed Abstract: 
  • Novel benzofuran-2-carboxylic acids, exemplified by 29, 38 and 39, have been discovered as potent Pim-1 inhibitors using fragment based screening followed by X-ray structure guided medicinal chemistry optimization. The compounds demonstrate potent in ...

    Novel benzofuran-2-carboxylic acids, exemplified by 29, 38 and 39, have been discovered as potent Pim-1 inhibitors using fragment based screening followed by X-ray structure guided medicinal chemistry optimization. The compounds demonstrate potent inhibition against Pim-1 and Pim-2 in enzyme assays. Compound 29 has been tested in the Ambit 442 kinase panel and demonstrates good selectivity for the Pim kinase family. X-ray structures of the inhibitor/Pim-1 binding complex reveal important salt-bridge and hydrogen bond interactions mediated by the compound's carboxylic acid and amino groups.


    Organizational Affiliation

    Department of Medicinal Chemistry, Drug and Biomaterial R&D, Genzyme Corp., 153 Second Avenue, Waltham, MA 02451, USA. yibin.xiang@genzyme.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase pim-1A299Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNJ
Query on UNJ

Download CCD File 
A
5-bromo-1-benzofuran-2-carboxylic acid
C9 H5 Br O3
QKUWZCOVKRUXKX-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 %)
UNJIC50:  8500   nM  BindingDB
UNJIC50:  8500   nM  Binding MOAD
UNJIC50 :  8500   nM  PDBBind
UNJIC50:  9000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.652α = 90
b = 97.652β = 90
c = 80.826γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-03-07 
  • Released Date: 2011-05-11 
  • Deposition Author(s): Liu, J.

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance