Structure of HSP90 with small molecule inhibitor bound

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Discovery of (2,4-Dihydroxy-5-Isopropylphenyl)-[5-(4-Methylpiperazin-1-Ylmethyl)-1,3-Dihydroisoindol-2-Yl]Methanone (at13387), a Novel Inhibitor of the Molecular Chaperone Hsp90 by Fragment Based Drug Design.

Woodhead, A.J.Angove, H.Carr, M.G.Chessari, G.Congreve, M.Coyle, J.E.Cosme, J.Graham, B.Day, P.J.Downham, R.Fazal, L.Feltell, R.Figueroa, E.Frederickson, M.Lewis, J.Mcmenamin, R.Murray, C.W.O'Brien, M.A.Parra, L.Patel, S.Phillips, T.Rees, D.C.Rich, S.Smith, D.Trewartha, G.Vinkovic, M.Williams, B.Woolford, A.J.

(2010) J Med Chem 53: 5956

  • DOI: https://doi.org/10.1021/jm100060b
  • Primary Citation of Related Structures:  
    2XAB, 2XJG, 2XJJ, 2XJX

  • PubMed Abstract: 

    Inhibitors of the molecular chaperone heat shock protein 90 (Hsp90) are currently generating significant interest in clinical development as potential treatments for cancer. In a preceding publication (DOI: 10.1021/jm100059d ) we describe Astex's approach to screening fragments against Hsp90 and the subsequent optimization of two hits into leads with inhibitory activities in the low nanomolar range. This paper describes the structure guided optimization of the 2,4-dihydroxybenzamide lead molecule 1 and details some of the drug discovery strategies employed in the identification of AT13387 (35), which has progressed through preclinical development and is currently being tested in man.

  • Organizational Affiliation

    Medicinal Chemistry, Astex Therapeutics, Ltd., Cambridge, UK. a.woodhead@astex-therapeutics.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
249Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
L81 PDBBind:  2XJJ Kd: 310 (nM) from 1 assay(s)
Binding MOAD:  2XJJ Kd: 310 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.326α = 82.59
b = 56.098β = 84.71
c = 61.607γ = 69.24
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other