2W1H

Fragment-Based Discovery of the Pyrazol-4-yl urea (AT9283), a Multi- targeted Kinase Inhibitor with Potent Aurora Kinase Activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery of the Pyrazol-4-Yl Urea (at9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity.

Howard, S.Berdini, V.Boulstridge, J.A.Carr, M.G.Cross, D.M.Curry, J.Devine, L.A.Early, T.R.Fazal, L.Gill, A.L.Heathcote, M.Maman, S.Matthews, J.E.Mcmenamin, R.L.Navarro, E.F.O'Brien, M.A.O'Reilly, M.Rees, D.C.Reule, M.Tisi, D.Williams, G.Vinkovic, M.Wyatt, P.G.

(2009) J Med Chem 52: 379

  • DOI: 10.1021/jm800984v
  • Primary Citation of Related Structures:  
    2W1C, 2W1D, 2W1E, 2W1F, 2W1G, 2W1H, 2W1I

  • PubMed Abstract: 
  • Here, we describe the identification of a clinical candidate via structure-based optimization of a ligand efficient pyrazole-benzimidazole fragment. Aurora kinases play a key role in the regulation of mitosis and in recent years have become attractive targets for the treatment of cancer ...

    Here, we describe the identification of a clinical candidate via structure-based optimization of a ligand efficient pyrazole-benzimidazole fragment. Aurora kinases play a key role in the regulation of mitosis and in recent years have become attractive targets for the treatment of cancer. X-ray crystallographic structures were generated using a novel soakable form of Aurora A and were used to drive the optimization toward potent (IC(50) approximately 3 nM) dual Aurora A/Aurora B inhibitors. These compounds inhibited growth and survival of HCT116 cells and produced the polyploid cellular phenotype typically associated with Aurora B kinase inhibition. Optimization of cellular activity and physicochemical properties ultimately led to the identification of compound 16 (AT9283). In addition to Aurora A and Aurora B, compound 16 was also found to inhibit a number of other kinases including JAK2 and Abl (T315I). This compound demonstrated in vivo efficacy in mouse xenograft models and is currently under evaluation in phase I clinical trials.


    Organizational Affiliation

    Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK. s.howard@astex-therapeutics.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L0F (Subject of Investigation/LOI)
Query on L0F

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(1H-BENZIMIDAZOL-2-YL)-1H-PYRAZOL-4-YL]BENZAMIDE
C17 H13 N5 O
FPKSFXFWECAIBR-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
L0H PDBBind:  2W1H IC50: 52 (nM) from 1 assay(s)
L0F BindingDB:  2W1H IC50: 52 (nM) from 1 assay(s)
Binding MOAD:  2W1H IC50: 52 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.57α = 90
b = 71.823β = 90
c = 72.476γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2012-05-16
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance