4FCR

Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization.

Davies, N.G.Browne, H.Davis, B.Drysdale, M.J.Foloppe, N.Geoffrey, S.Gibbons, B.Hart, T.Hubbard, R.Jensen, M.R.Mansell, H.Massey, A.Matassova, N.Moore, J.D.Murray, J.Pratt, R.Ray, S.Robertson, A.Roughley, S.D.Schoepfer, J.Scriven, K.Simmonite, H.Stokes, S.Surgenor, A.Webb, P.Wood, M.Wright, L.Brough, P.

(2012) Bioorg Med Chem 20: 6770-6789

  • DOI: 10.1016/j.bmc.2012.08.050
  • Primary Citation of Related Structures:  
    4FCP, 4FCQ, 4FCR

  • PubMed Abstract: 
  • Inhibitors of the Hsp90 molecular chaperone are showing promise as anti-cancer agents. Here we describe a series of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors that were identified following structure-driven optimization o ...

    Inhibitors of the Hsp90 molecular chaperone are showing promise as anti-cancer agents. Here we describe a series of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors that were identified following structure-driven optimization of purine hits revealed by NMR based screening of a proprietary fragment library. Ligand-Hsp90 X-ray structures combined with molecular modeling led to the rational displacement of a conserved water molecule leading to enhanced affinity for Hsp90 as measured by fluorescence polarization, isothermal titration calorimetry and surface plasmon resonance assays. This displacement was achieved with a nitrile group, presenting an example of efficient gain in binding affinity with minimal increase in molecular weight. Some compounds in this chemical series inhibit the proliferation of human cancer cell lines in vitro and cause depletion of oncogenic Hsp90 client proteins and concomitant elevation of the co-chaperone Hsp70. In addition, one compound was demonstrated to be orally bioavailable in the mouse. This work demonstrates the power of structure-based design for the rapid evolution of potent Hsp90 inhibitors and the importance of considering conserved water molecules in drug design.


    Organizational Affiliation

    Vernalis Ltd., Granta Park, Great Abington, Cambridge, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA236Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
NIH Common Fund Data Resources
PHAROS  P07900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0TM
Query on 0TM

Download CCD File 
A
2-{[4-(2-chloro-4,5-dimethoxyphenyl)-5-cyano-7H-pyrrolo[2,3-d]pyrimidin-2-yl]sulfanyl}-N,N-dimethylacetamide
C19 H18 Cl N5 O3 S
JLZNENFSPWZCAG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0TMKd :  0.4000000059604645   nM  PDBBind
0TMKd:  0.4000000059604645   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.659α = 90
b = 89.764β = 90
c = 98.251γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references