Orally Active 2-Amino Thienopyrimidine Inhibitors of the Hsp90 Chaperone

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 

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Combining Hit Identification Strategies: Fragment- Based and in Silico Approaches to Orally Active 2-Aminothieno[2,3-D]Pyrimidine Inhibitors of the Hsp90 Molecular Chaperone.

Brough, P.A.Barril, X.Borgognoni, J.Chene, P.Davies, N.G.M.Davis, B.Drysdale, M.J.Dymock, B.Eccles, S.A.Garcia-Echeverria, C.Fromont, C.Hayes, A.Hubbard, R.E.Jordan, A.M.Jensen, M.R.Massey, A.Merrett, A.Padfield, A.Parsons, R.Radimerski, T.Raynaud, F.I.Robertson, A.Roughley, S.D.Schoepfer, J.Simmonite, H.Sharp, S.Y.Surgenor, A.Valenti, M.Walls, S.Webb, P.Wood, M.Workman, P.Wright, L.M.

(2009) J Med Chem 52: 4794

  • DOI: https://doi.org/10.1021/jm900357y
  • Primary Citation of Related Structures:  
    2WI1, 2WI2, 2WI3, 2WI4, 2WI5, 2WI6, 2WI7

  • PubMed Abstract: 

    Inhibitors of the Hsp90 molecular chaperone are showing considerable promise as potential molecular therapeutic agents for the treatment of cancer. Here we describe novel 2-aminothieno[2,3-d]pyrimidine ATP competitive Hsp90 inhibitors, which were designed by combining structural elements of distinct low affinity hits generated from fragment-based and in silico screening exercises in concert with structural information from X-ray protein crystallography. Examples from this series have high affinity (IC50 = 50-100 nM) for Hsp90 as measured in a fluorescence polarization (FP) competitive binding assay and are active in human cancer cell lines where they inhibit cell proliferation and exhibit a characteristic profile of depletion of oncogenic proteins and concomitant elevation of Hsp72. Several examples (34a, 34d and 34i) caused tumor growth regression at well tolerated doses when administered orally in a human BT474 human breast cancer xenograft model.

  • Organizational Affiliation

    Vernalis Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, UK. p.brough@vernalis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT SHOCK PROTEIN HSP 90-ALPHA236Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2KL

Download Ideal Coordinates CCD File 
B [auth A]2-amino-4-[2,4-dichloro-5-(2-pyrrolidin-1-ylethoxy)phenyl]-N-ethylthieno[2,3-d]pyrimidine-6-carboxamide
C21 H23 Cl2 N5 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
2KL BindingDB:  2WI7 IC50: 58 (nM) from 1 assay(s)
PDBBind:  2WI7 IC50: 58 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.795α = 90
b = 90.416β = 90
c = 99.29γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description