3R02

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase pim-1
A
299Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNM
Query on UNM

Download SDF File 
Download CCD File 
A
7-[(cis-4-aminocyclohexyl)amino]-5-bromo-1-benzofuran-2-carboxylic acid
C15 H17 Br N2 O3
BLBAWGODFTZAEY-PHIMTYICSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UNMIC50: 1 nM (100) BINDINGDB
UNMIC50: 1 nM BINDINGMOAD
UNMIC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.170α = 90.00
b = 97.170β = 90.00
c = 81.190γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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