3R01

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase pim-1299Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UNE PDBBind:  3R01 IC50: 5800 (nM) from 1 assay(s)
BindingDB:  3R01 IC50: min: 5800, max: 6000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.943α = 90
b = 97.943β = 90
c = 80.747γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations